Query 024081
Match_columns 272
No_of_seqs 279 out of 933
Neff 5.0
Searched_HMMs 46136
Date Fri Mar 29 08:49:34 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/024081.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/024081hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd00073 H15 linker histone 1 a 99.8 4.3E-21 9.2E-26 149.9 8.8 71 109-179 2-78 (88)
2 smart00526 H15 Domain in histo 99.8 3.5E-21 7.5E-26 142.4 7.8 64 109-172 2-66 (66)
3 PF00538 Linker_histone: linke 99.8 4.1E-21 8.9E-26 146.2 7.5 69 110-178 1-77 (77)
4 KOG4012 Histone H1 [Chromatin 99.5 2.7E-14 5.9E-19 130.4 7.3 77 104-180 37-120 (243)
5 PF00249 Myb_DNA-binding: Myb- 99.3 3.3E-12 7.2E-17 88.7 2.9 47 5-57 1-48 (48)
6 PLN03212 Transcription repress 99.0 3.8E-10 8.2E-15 103.4 6.2 107 1-160 21-129 (249)
7 smart00717 SANT SANT SWI3, AD 99.0 6.4E-10 1.4E-14 74.3 4.5 48 5-58 1-48 (49)
8 cd00167 SANT 'SWI3, ADA2, N-Co 98.9 2.7E-09 5.8E-14 70.4 4.1 45 7-57 1-45 (45)
9 PF13921 Myb_DNA-bind_6: Myb-l 98.8 4E-09 8.7E-14 75.7 3.9 44 8-58 1-44 (60)
10 PLN03091 hypothetical protein; 98.8 6.9E-09 1.5E-13 101.7 6.5 104 4-160 13-118 (459)
11 PLN03212 Transcription repress 98.7 8.1E-08 1.8E-12 88.3 8.4 51 3-60 76-126 (249)
12 KOG0048 Transcription factor, 98.6 3.1E-08 6.7E-13 90.0 5.0 105 5-162 9-115 (238)
13 PLN03091 hypothetical protein; 98.4 2.5E-07 5.3E-12 91.0 4.6 53 3-62 65-117 (459)
14 KOG0048 Transcription factor, 97.9 9.4E-06 2E-10 73.8 3.2 51 3-60 60-110 (238)
15 TIGR01557 myb_SHAQKYF myb-like 97.8 3.4E-05 7.3E-10 56.3 4.8 48 3-55 1-52 (57)
16 KOG0051 RNA polymerase I termi 97.5 6.1E-05 1.3E-09 76.9 2.7 50 4-61 383-432 (607)
17 KOG0049 Transcription factor, 97.4 0.00016 3.5E-09 74.3 4.0 51 2-58 357-407 (939)
18 KOG0457 Histone acetyltransfer 97.1 0.00033 7.1E-09 69.0 3.1 49 6-60 73-121 (438)
19 PF13837 Myb_DNA-bind_4: Myb/S 96.9 0.00019 4.2E-09 54.6 -0.1 54 5-60 1-67 (90)
20 KOG0049 Transcription factor, 96.9 0.00043 9.3E-09 71.3 1.8 49 3-57 410-458 (939)
21 PF09111 SLIDE: SLIDE; InterP 96.4 0.0015 3.3E-08 54.1 1.7 57 3-59 47-112 (118)
22 PF13873 Myb_DNA-bind_5: Myb/S 95.9 0.0049 1.1E-07 46.2 2.1 54 5-60 2-72 (78)
23 KOG1279 Chromatin remodeling f 95.2 0.019 4.1E-07 58.2 4.0 49 4-59 252-300 (506)
24 PF13325 MCRS_N: N-terminal re 95.1 0.014 3E-07 52.6 2.2 56 4-60 72-129 (199)
25 KOG0050 mRNA splicing protein 95.0 0.0094 2E-07 60.3 1.2 49 6-60 8-56 (617)
26 PLN03142 Probable chromatin-re 94.8 0.026 5.6E-07 61.6 4.0 60 4-63 925-990 (1033)
27 COG5147 REB1 Myb superfamily p 94.6 0.0093 2E-07 60.4 -0.1 49 4-60 290-338 (512)
28 PF08074 CHDCT2: CHDCT2 (NUC03 94.2 0.026 5.6E-07 49.6 1.9 47 6-53 4-58 (173)
29 COG5259 RSC8 RSC chromatin rem 93.5 0.056 1.2E-06 54.3 3.0 45 6-57 280-324 (531)
30 PF00250 Fork_head: Fork head 92.8 0.2 4.2E-06 40.0 4.6 57 111-171 3-63 (96)
31 PF10264 Stork_head: Winged he 92.6 0.54 1.2E-05 36.8 6.7 66 112-177 10-77 (80)
32 COG5114 Histone acetyltransfer 92.6 0.073 1.6E-06 51.4 2.2 46 7-58 65-110 (432)
33 cd00059 FH Forkhead (FH), also 92.5 0.13 2.8E-06 39.7 3.1 47 111-158 3-53 (78)
34 PF14338 Mrr_N: Mrr N-terminal 92.1 0.4 8.7E-06 37.3 5.5 66 113-178 1-82 (92)
35 COG5147 REB1 Myb superfamily p 91.3 0.074 1.6E-06 54.0 0.6 50 4-59 19-68 (512)
36 KOG4282 Transcription factor G 90.6 0.22 4.9E-06 47.3 3.2 62 5-68 54-124 (345)
37 smart00339 FH FORKHEAD. FORKHE 89.8 0.41 8.9E-06 37.7 3.6 46 112-158 4-53 (89)
38 KOG0384 Chromodomain-helicase 89.2 0.18 3.8E-06 55.8 1.4 52 6-57 1134-1191(1373)
39 PF08914 Myb_DNA-bind_2: Rap1 87.9 0.64 1.4E-05 34.8 3.3 50 5-59 2-59 (65)
40 KOG0051 RNA polymerase I termi 86.5 0.61 1.3E-05 48.3 3.3 53 3-61 434-511 (607)
41 KOG2656 DNA methyltransferase 85.3 0.88 1.9E-05 45.1 3.6 51 6-57 131-181 (445)
42 PF12776 Myb_DNA-bind_3: Myb/S 79.3 1.6 3.4E-05 33.4 2.4 52 7-60 1-65 (96)
43 PF09420 Nop16: Ribosome bioge 76.8 5.4 0.00012 34.4 5.1 51 4-57 113-163 (164)
44 KOG0050 mRNA splicing protein 75.4 2.2 4.7E-05 43.8 2.6 48 5-60 59-106 (617)
45 PF08672 APC2: Anaphase promot 70.6 3.8 8.2E-05 30.1 2.3 26 151-176 35-60 (60)
46 PF11839 DUF3359: Protein of u 69.4 34 0.00074 27.7 7.7 50 209-258 35-84 (96)
47 PF04504 DUF573: Protein of un 65.5 5.5 0.00012 31.8 2.5 57 4-60 3-65 (98)
48 PF14947 HTH_45: Winged helix- 62.3 7 0.00015 29.5 2.4 56 115-178 5-60 (77)
49 COG5118 BDP1 Transcription ini 60.7 10 0.00022 37.8 3.8 50 4-60 364-413 (507)
50 PRK13923 putative spore coat p 60.2 3 6.4E-05 37.0 0.1 58 1-59 1-58 (170)
51 PF05928 Zea_mays_MuDR: Zea ma 60.1 21 0.00045 31.9 5.2 27 211-237 12-38 (207)
52 PF05402 PqqD: Coenzyme PQQ sy 58.0 19 0.00041 25.7 4.0 39 129-167 28-67 (68)
53 PF11626 Rap1_C: TRF2-interact 46.5 19 0.00041 27.9 2.6 21 5-25 47-75 (87)
54 smart00550 Zalpha Z-DNA-bindin 45.9 87 0.0019 22.9 6.0 59 111-177 4-65 (68)
55 PF05732 RepL: Firmicute plasm 43.1 67 0.0015 27.9 5.8 63 114-180 42-119 (165)
56 PF08784 RPA_C: Replication pr 41.3 57 0.0012 25.4 4.6 53 110-169 44-97 (102)
57 PF13325 MCRS_N: N-terminal re 40.7 42 0.00091 30.5 4.2 49 7-60 1-49 (199)
58 PF05066 HARE-HTH: HB1, ASXL, 39.8 77 0.0017 23.1 4.9 62 113-176 2-69 (72)
59 COG4742 Predicted transcriptio 38.6 42 0.0009 31.7 4.0 48 123-178 20-67 (260)
60 cd00092 HTH_CRP helix_turn_hel 37.3 39 0.00084 23.5 2.9 41 131-178 26-67 (67)
61 PF06969 HemN_C: HemN C-termin 36.4 60 0.0013 23.0 3.8 48 125-178 15-62 (66)
62 PF11839 DUF3359: Protein of u 33.2 2.5E+02 0.0055 22.7 7.1 35 215-249 48-82 (96)
63 PF08220 HTH_DeoR: DeoR-like h 32.4 52 0.0011 23.3 2.8 27 152-178 29-55 (57)
64 cd01392 HTH_LacI Helix-turn-he 31.2 43 0.00093 22.4 2.2 36 125-160 3-38 (52)
65 smart00346 HTH_ICLR helix_turn 30.8 1.6E+02 0.0035 21.7 5.5 52 118-178 10-63 (91)
66 PF13463 HTH_27: Winged helix 29.5 85 0.0018 21.9 3.6 47 116-171 6-52 (68)
67 smart00419 HTH_CRP helix_turn_ 29.1 64 0.0014 20.8 2.7 26 151-176 22-47 (48)
68 PF01325 Fe_dep_repress: Iron 28.9 2.2E+02 0.0047 20.5 5.6 47 114-170 9-55 (60)
69 PF01726 LexA_DNA_bind: LexA D 27.9 1.4E+02 0.0029 22.0 4.5 22 152-173 41-62 (65)
70 PF08343 RNR_N: Ribonucleotide 27.8 48 0.001 25.9 2.1 50 118-169 3-59 (82)
71 KOG3614 Ca2+/Mg2+-permeable ca 27.7 1.2E+02 0.0027 34.8 5.9 34 231-264 603-636 (1381)
72 CHL00137 rps13 ribosomal prote 27.2 88 0.0019 26.1 3.8 49 129-177 49-97 (122)
73 PF15054 DUF4535: Domain of un 26.6 32 0.00069 24.3 0.8 20 139-159 15-34 (46)
74 PF03234 CDC37_N: Cdc37 N term 26.4 1.3E+02 0.0027 26.8 4.8 41 104-144 99-140 (177)
75 PF00356 LacI: Bacterial regul 26.2 41 0.00088 23.3 1.3 39 122-160 2-40 (46)
76 smart00354 HTH_LACI helix_turn 25.7 55 0.0012 23.9 2.0 38 123-160 4-41 (70)
77 PF07106 TBPIP: Tat binding pr 25.4 60 0.0013 27.8 2.5 36 134-169 4-50 (169)
78 TIGR02894 DNA_bind_RsfA transc 24.8 36 0.00078 30.0 1.1 50 5-60 4-58 (161)
79 PF02295 z-alpha: Adenosine de 24.7 1.5E+02 0.0032 22.0 4.2 51 114-172 5-55 (66)
80 PF12363 DUF3647: Phage protei 24.6 2E+02 0.0043 23.3 5.3 53 114-168 53-105 (113)
81 PF13412 HTH_24: Winged helix- 23.5 1.5E+02 0.0033 19.6 3.8 37 124-167 11-47 (48)
82 smart00347 HTH_MARR helix_turn 23.1 1.3E+02 0.0027 22.1 3.7 48 114-171 11-58 (101)
83 smart00595 MADF subfamily of S 22.8 36 0.00078 25.5 0.6 33 27-66 29-61 (89)
84 PF00392 GntR: Bacterial regul 22.6 2.6E+02 0.0056 19.7 5.1 53 116-172 7-59 (64)
85 smart00420 HTH_DEOR helix_turn 22.4 1.8E+02 0.004 18.7 4.0 40 128-174 12-51 (53)
86 KOG2009 Transcription initiati 22.3 1.1E+02 0.0024 32.1 4.1 50 4-60 408-457 (584)
87 PF08944 p47_phox_C: NADPH oxi 21.1 43 0.00093 24.8 0.7 8 257-264 38-45 (58)
88 PF10929 DUF2811: Protein of u 20.1 1.3E+02 0.0027 22.3 2.9 28 134-165 12-42 (57)
89 PF12029 DUF3516: Domain of un 20.1 2.1E+02 0.0045 29.3 5.4 53 115-171 61-116 (461)
90 PF08671 SinI: Anti-repressor 20.1 2E+02 0.0043 18.5 3.5 25 114-143 5-29 (30)
No 1
>cd00073 H15 linker histone 1 and histone 5 domains; the basic subunit of chromatin is the nucleosome, consisting of an octamer of core histones, two full turns of DNA, a linker histone (H1 or H5) and a variable length of linker DNA; H1/H5 are chromatin-associated proteins that bind to the exterior of nucleosomes and dramatically stabilize the highly condensed states of chromatin fibers; stabilization of higher order folding occurs through electrostatic neutralization of the linker DNA segments, through a highly positively charged carboxy- terminal domain known as the AKP helix (Ala, Lys, Pro); thought to be involved in specific protein-protein and protein-DNA interactions and play a role in suppressing core histone tail domain acetylation in the chromatin fiber
Probab=99.84 E-value=4.3e-21 Score=149.92 Aligned_cols=71 Identities=42% Similarity=0.649 Sum_probs=67.0
Q ss_pred CCCCCHHHHHHHHHHhcCCCCCCCHHHHHHHHHhhcCCC-ccHHHHHHHHHHhhhccCceeeec-----cccccCCc
Q 024081 109 SSAPKYNALIFEAISALKEPNGSDVSAILSYIEQRLEVP-PNFRRLLSSRLRRLVAQEKLEKVQ-----NCFKVKED 179 (272)
Q Consensus 109 ~shp~y~~MI~EAI~~Lker~GSS~~AI~kyIe~~y~v~-~nf~~~L~~~LKrlV~~GkLvkvK-----~sykl~~~ 179 (272)
.+||+|.+||+|||.+|+||+|||+++|++||+++|.+. ++|+.+|+.+|+++|++|.|++++ |+|+|++.
T Consensus 2 ~~hP~y~~MI~eAI~~l~er~GsS~~aI~kyI~~~y~~~~~~~~~~l~~aLkk~v~~G~l~~~kG~g~~gsfkl~~~ 78 (88)
T cd00073 2 PSHPPYSEMVTEAIKALKERKGSSLQAIKKYIEAKYKVDDENFNKLLKLALKKGVAKGKLVQVKGTGASGSFKLSKK 78 (88)
T ss_pred CCCCCHHHHHHHHHHHcCCCCCcCHHHHHHHHHHHCCcchHHHHHHHHHHHHHHHHCCCeEeecCCCCccceEeCCC
Confidence 579999999999999999999999999999999999764 999999999999999999999999 89999743
No 2
>smart00526 H15 Domain in histone families 1 and 5.
Probab=99.84 E-value=3.5e-21 Score=142.37 Aligned_cols=64 Identities=52% Similarity=0.736 Sum_probs=61.5
Q ss_pred CCCCCHHHHHHHHHHhcCCCCCCCHHHHHHHHHhhcCC-CccHHHHHHHHHHhhhccCceeeecc
Q 024081 109 SSAPKYNALIFEAISALKEPNGSDVSAILSYIEQRLEV-PPNFRRLLSSRLRRLVAQEKLEKVQN 172 (272)
Q Consensus 109 ~shp~y~~MI~EAI~~Lker~GSS~~AI~kyIe~~y~v-~~nf~~~L~~~LKrlV~~GkLvkvK~ 172 (272)
.+||+|.+||+|||.+|+||+|||+++|++||+++|++ +++|+.+|+.+|+++|++|.|+|++|
T Consensus 2 ~~hP~~~~mI~eAI~~l~er~GsS~~aI~kyi~~~~~~~~~~~~~~l~~~Lk~~v~~G~l~q~kg 66 (66)
T smart00526 2 PSHPPYSEMITEAISALKERKGSSLQAIKKYIEANYKVLPNNFRSLLKLALKKLVASGKLVQVKG 66 (66)
T ss_pred CCCCCHHHHHHHHHHHcCCCCCCCHHHHHHHHHHhCCCChHHHHHHHHHHHHHHHhcCceeecCC
Confidence 57999999999999999999999999999999999975 88999999999999999999999986
No 3
>PF00538 Linker_histone: linker histone H1 and H5 family; InterPro: IPR005818 Histone proteins have central roles in both chromatin organisation (as structural units of the nucleosome) and gene regulation (as dynamic components that have a direct impact on DNA transcription and replication). Eukaryotic DNA wraps around a histone octamer to form a nucleosome, the first order of compaction of eukaryotic chromatin. The core histone octamer is composed of a central H3-H4 tetramer and two flanking H2A-H2B dimers. Each of the core histone contains a common structural motif, called the histone fold, which facilitates the interactions between the individual core histones. In addition to the core histones, there is a "linker histone" called H1 (or H5 in avian species). The linker histones present in all multicellular eukaryotes are the most divergent group of histones, with numerous cell type- and stage-specific variant. Linker histone H1 is an essential component of chromatin structure. H1 links nucleosomes into higher order structures. Histone H5 performs the same function as histone H1, and replaces H1 in certain cells. The structure of GH5, the globular domain of the linker histone H5 is known [, ]. The fold is similar to the DNA-binding domain of the catabolite gene activator protein, CAP, thus providing a possible model for the binding of GH5 to DNA. The linker histones, which do not contain the histone fold motif, are critical to the higher-order compaction of chromatin, because they bind to internucleosomal DNA and facilitate interactions between individual nucleosomes. In addition, H1 variants have been shown to be involved in the regulation of developmental genes. A common feature of this protein family is a tripartite structure in which a globular (H15) domain of about 80 amino acids is flanked by two less structured N- and C-terminal tails. The H15 domain is also characterised by high sequence homology among the family of linker histones. The highly conserved H15 domain is essential for the binding of H1 or H5 to the nucleosome. It consists of a three helix bundle (I-III), with a beta-hairpin at the C terminus. There is also a short three-residue stretch between helices I and II that is in the beta-strand conformation. Together with the C-terminal beta-hairpin, this strand forms the third strand of an antiparallel beta-sheet [, , , ]. Proteins known to contain a H15 domain are: - Eukaryotic histone H1. The histones H1 constitute a family with many variants, differing in their affinity for chromatin. Several variants are simultaneously present in a single cell. For example, the nucleated erythrocytes of birds contain both H1 and H5, the latter being an extreme variant of H1. - Eukaryotic MHYST family of histone acetyltransferase. Histone acetyltransferases transfer an acetyl group from acetyl-CoA to the epsylon- amino group of lysine within the basic NH2-termini of histones, which bind the acidic phosphates of DNA []. This entry represents the H15 domain.; GO: 0003677 DNA binding, 0006334 nucleosome assembly, 0000786 nucleosome, 0005634 nucleus; PDB: 2LSO_A 2RQP_A 1UHM_A 1UST_A 1GHC_A 1HST_A 1YQA_A 1USS_A.
Probab=99.84 E-value=4.1e-21 Score=146.24 Aligned_cols=69 Identities=42% Similarity=0.680 Sum_probs=64.2
Q ss_pred CCCCHHHHHHHHHHhcCCCCCCCHHHHHHHHHhhcC--CCc-cHHHHHHHHHHhhhccCceeeec-----cccccCC
Q 024081 110 SAPKYNALIFEAISALKEPNGSDVSAILSYIEQRLE--VPP-NFRRLLSSRLRRLVAQEKLEKVQ-----NCFKVKE 178 (272)
Q Consensus 110 shp~y~~MI~EAI~~Lker~GSS~~AI~kyIe~~y~--v~~-nf~~~L~~~LKrlV~~GkLvkvK-----~sykl~~ 178 (272)
+||+|.+||+|||.+|+||+|||+++|.+||+++|+ +++ +|+.+|+.+|+++|++|.|++++ |+|||+.
T Consensus 1 shP~y~~mI~eAI~~l~er~GsS~~aI~kyI~~~y~~~~~~~~~~~~l~~aLk~~v~~G~l~~~kg~G~sgsfkl~k 77 (77)
T PF00538_consen 1 SHPPYSDMILEAIKALKERKGSSLQAIKKYIKAKYKVDLNPANFKSRLKRALKRGVEKGKLVQVKGKGASGSFKLSK 77 (77)
T ss_dssp -SSCHHHHHHHHHHHCCSSSSEEHHHHHHHHHHHSSCCCCHTTHHHHHHHHHHHHHHCTSEEECSCSTTSSEEEESS
T ss_pred CCCCHHHHHHHHHHHcCCCCCCCHHHHHHHHHHhcCcCCChHHHHHHHHHHHHHHHHCCcEEeecccCCccceecCC
Confidence 599999999999999999999999999999999996 444 89999999999999999999999 8999963
No 4
>KOG4012 consensus Histone H1 [Chromatin structure and dynamics]
Probab=99.51 E-value=2.7e-14 Score=130.45 Aligned_cols=77 Identities=31% Similarity=0.422 Sum_probs=68.6
Q ss_pred CCCCCCCCCCHHHHHHHHHHhcCCCCCCCHHHHHHHHHhhc-CC-CccHHHHHHHHHHhhhccCceeeecc-----cccc
Q 024081 104 DESARSSAPKYNALIFEAISALKEPNGSDVSAILSYIEQRL-EV-PPNFRRLLSSRLRRLVAQEKLEKVQN-----CFKV 176 (272)
Q Consensus 104 ~~~~~~shp~y~~MI~EAI~~Lker~GSS~~AI~kyIe~~y-~v-~~nf~~~L~~~LKrlV~~GkLvkvK~-----sykl 176 (272)
.......||+|.+||.|||.+|+||+|+|+.+|++||.++| +. -++|+.+|+..|+++|.+|.|+|++| +|+|
T Consensus 37 ~~k~~a~~P~~~~mi~eAi~a~keR~GsS~aAikK~i~~~Y~g~~v~k~n~~lk~alK~~v~~g~l~QtkG~GAsGsFk~ 116 (243)
T KOG4012|consen 37 KVKKKAAHPPYSEMITEAISALKERKGSSLAAIKKYIAANYPGDDVEKNNSRLKLALKKGVSKGVLVQTKGTGASGSFKL 116 (243)
T ss_pred ccccccCCCcHHHHHHHHHHHhhhcccchHHHHHHHHhhcCccchhhhhhHHHHHHHHhhhccCceeeeccCCccccccc
Confidence 34456689999999999999999999999999999999999 11 36789999999999999999999986 9999
Q ss_pred CCcc
Q 024081 177 KEDA 180 (272)
Q Consensus 177 ~~~~ 180 (272)
....
T Consensus 117 ~KK~ 120 (243)
T KOG4012|consen 117 AKKA 120 (243)
T ss_pred cccc
Confidence 8755
No 5
>PF00249 Myb_DNA-binding: Myb-like DNA-binding domain; InterPro: IPR014778 The retroviral oncogene v-myb, and its cellular counterpart c-myb, encode nuclear DNA-binding proteins. These belong to the SANT domain family that specifically recognise the sequence YAAC(G/T)G [, ]. In myb, one of the most conserved regions consisting of three tandem repeats has been shown to be involved in DNA-binding [].; PDB: 1X41_A 2XAF_B 2XAG_B 2XAH_B 2UXN_B 2Y48_B 2XAQ_B 2X0L_B 2IW5_B 2XAJ_B ....
Probab=99.25 E-value=3.3e-12 Score=88.67 Aligned_cols=47 Identities=30% Similarity=0.623 Sum_probs=41.5
Q ss_pred CCCCCHHHHHHHHHHHHhhCCCCccccccccccCccCC-CCCHHhHHHHHHhhc
Q 024081 5 KQKWTAEEEEALRAGVAKHGTGKWKNIQRDPEFNPFLF-SRSNIDLKDKWRNMS 57 (272)
Q Consensus 5 r~~WT~EEe~~L~~GV~KyG~GkW~~I~~~~~f~~~l~-~RT~vdLKDKWRnl~ 57 (272)
|++||+||++.|+++|.+||.++|..|+.. ++ +||..||+++|+++.
T Consensus 1 r~~Wt~eE~~~l~~~v~~~g~~~W~~Ia~~------~~~~Rt~~qc~~~~~~~~ 48 (48)
T PF00249_consen 1 RGPWTEEEDEKLLEAVKKYGKDNWKKIAKR------MPGGRTAKQCRSRYQNLL 48 (48)
T ss_dssp S-SS-HHHHHHHHHHHHHSTTTHHHHHHHH------HSSSSTHHHHHHHHHHHT
T ss_pred CCCCCHHHHHHHHHHHHHhCCcHHHHHHHH------cCCCCCHHHHHHHHHhhC
Confidence 689999999999999999999889999994 45 999999999999874
No 6
>PLN03212 Transcription repressor MYB5; Provisional
Probab=99.02 E-value=3.8e-10 Score=103.42 Aligned_cols=107 Identities=24% Similarity=0.404 Sum_probs=79.1
Q ss_pred CCCCCCCCCHHHHHHHHHHHHhhCCCCccccccccccCccCCCCCHHhHHHHHHhhccCchhhhcccCCCCCCCCCCCCC
Q 024081 1 MGNPKQKWTAEEEEALRAGVAKHGTGKWKNIQRDPEFNPFLFSRSNIDLKDKWRNMSVSAPREKSRTLKPKAGSDAPAVP 80 (272)
Q Consensus 1 mg~~r~~WT~EEe~~L~~GV~KyG~GkW~~I~~~~~f~~~l~~RT~vdLKDKWRnl~~~~~r~k~~~~~~~~~~~~~~~~ 80 (272)
+|-+|++||+|||+.|+..|++||.++|..|... +..+||+.||++||.|.+.+.. .+.+-+ .
T Consensus 21 ~glKRg~WT~EEDe~L~~lV~kyG~~nW~~IAk~-----~g~gRT~KQCReRW~N~L~P~I--------~kgpWT-~--- 83 (249)
T PLN03212 21 MGMKRGPWTVEEDEILVSFIKKEGEGRWRSLPKR-----AGLLRCGKSCRLRWMNYLRPSV--------KRGGIT-S--- 83 (249)
T ss_pred CCCcCCCCCHHHHHHHHHHHHHhCcccHHHHHHh-----hhcCCCcchHHHHHHHhhchhc--------ccCCCC-h---
Confidence 4778999999999999999999999999999973 1258999999999999997753 122220 0
Q ss_pred CCCCCCCCCCCccCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHhcCCCCCCCHHHHHHHHHhhcC--CCccHHHHHHHHH
Q 024081 81 LSTPQTSALPAAVPIDASADPITDESARSSAPKYNALIFEAISALKEPNGSDVSAILSYIEQRLE--VPPNFRRLLSSRL 158 (272)
Q Consensus 81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~shp~y~~MI~EAI~~Lker~GSS~~AI~kyIe~~y~--v~~nf~~~L~~~L 158 (272)
-=+++|++.+.. -|.....|++++..+.+ +-..|..+|+..+
T Consensus 84 --------------------------------EED~lLlel~~~----~GnKWs~IAk~LpGRTDnqIKNRWns~LrK~l 127 (249)
T PLN03212 84 --------------------------------DEEDLILRLHRL----LGNRWSLIAGRIPGRTDNEIKNYWNTHLRKKL 127 (249)
T ss_pred --------------------------------HHHHHHHHHHHh----ccccHHHHHhhcCCCCHHHHHHHHHHHHhHHH
Confidence 127788877665 56678999999977653 2334455555554
Q ss_pred Hh
Q 024081 159 RR 160 (272)
Q Consensus 159 Kr 160 (272)
++
T Consensus 128 ~r 129 (249)
T PLN03212 128 LR 129 (249)
T ss_pred Hh
Confidence 43
No 7
>smart00717 SANT SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains.
Probab=98.98 E-value=6.4e-10 Score=74.33 Aligned_cols=48 Identities=33% Similarity=0.664 Sum_probs=43.7
Q ss_pred CCCCCHHHHHHHHHHHHhhCCCCccccccccccCccCCCCCHHhHHHHHHhhcc
Q 024081 5 KQKWTAEEEEALRAGVAKHGTGKWKNIQRDPEFNPFLFSRSNIDLKDKWRNMSV 58 (272)
Q Consensus 5 r~~WT~EEe~~L~~GV~KyG~GkW~~I~~~~~f~~~l~~RT~vdLKDKWRnl~~ 58 (272)
+.+||++|+..|+.++..||.++|..|... +++||+.+|+++|+++.+
T Consensus 1 ~~~Wt~~E~~~l~~~~~~~g~~~w~~Ia~~------~~~rt~~~~~~~~~~~~~ 48 (49)
T smart00717 1 KGEWTEEEDELLIELVKKYGKNNWEKIAKE------LPGRTAEQCRERWNNLLK 48 (49)
T ss_pred CCCCCHHHHHHHHHHHHHHCcCCHHHHHHH------cCCCCHHHHHHHHHHHcC
Confidence 468999999999999999997799999983 569999999999999865
No 8
>cd00167 SANT 'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric DNA tandem repeatsas part of the capping complex. Binding is sequence dependent for repeats which contain the G/C rich motif [C2-3 A (CA)1-6]. The domain is also found in regulatory transcriptional repressor complexes where it also binds DNA.
Probab=98.86 E-value=2.7e-09 Score=70.41 Aligned_cols=45 Identities=36% Similarity=0.761 Sum_probs=41.1
Q ss_pred CCCHHHHHHHHHHHHhhCCCCccccccccccCccCCCCCHHhHHHHHHhhc
Q 024081 7 KWTAEEEEALRAGVAKHGTGKWKNIQRDPEFNPFLFSRSNIDLKDKWRNMS 57 (272)
Q Consensus 7 ~WT~EEe~~L~~GV~KyG~GkW~~I~~~~~f~~~l~~RT~vdLKDKWRnl~ 57 (272)
+||.+|+..|+.++.+||.++|..|... +++||..+|+++|.++.
T Consensus 1 ~Wt~eE~~~l~~~~~~~g~~~w~~Ia~~------~~~rs~~~~~~~~~~~~ 45 (45)
T cd00167 1 PWTEEEDELLLEAVKKYGKNNWEKIAKE------LPGRTPKQCRERWRNLL 45 (45)
T ss_pred CCCHHHHHHHHHHHHHHCcCCHHHHHhH------cCCCCHHHHHHHHHHhC
Confidence 5999999999999999998899999983 56899999999998863
No 9
>PF13921 Myb_DNA-bind_6: Myb-like DNA-binding domain; PDB: 1A5J_A 1MBH_A 1GV5_A 1H89_C 1IDY_A 1MBK_A 1IDZ_A 1H88_C 1GVD_A 1MBG_A ....
Probab=98.81 E-value=4e-09 Score=75.73 Aligned_cols=44 Identities=39% Similarity=0.664 Sum_probs=36.7
Q ss_pred CCHHHHHHHHHHHHhhCCCCccccccccccCccCCCCCHHhHHHHHHhhcc
Q 024081 8 WTAEEEEALRAGVAKHGTGKWKNIQRDPEFNPFLFSRSNIDLKDKWRNMSV 58 (272)
Q Consensus 8 WT~EEe~~L~~GV~KyG~GkW~~I~~~~~f~~~l~~RT~vdLKDKWRnl~~ 58 (272)
||.||++.|+.+|.+||. +|..|... |.+||+.+|++||++.+.
T Consensus 1 WT~eEd~~L~~~~~~~g~-~W~~Ia~~------l~~Rt~~~~~~r~~~~l~ 44 (60)
T PF13921_consen 1 WTKEEDELLLELVKKYGN-DWKKIAEH------LGNRTPKQCRNRWRNHLR 44 (60)
T ss_dssp S-HHHHHHHHHHHHHHTS--HHHHHHH------STTS-HHHHHHHHHHTTS
T ss_pred CCHHHHHHHHHHHHHHCc-CHHHHHHH------HCcCCHHHHHHHHHHHCc
Confidence 999999999999999996 99999983 557999999999999443
No 10
>PLN03091 hypothetical protein; Provisional
Probab=98.80 E-value=6.9e-09 Score=101.67 Aligned_cols=104 Identities=22% Similarity=0.373 Sum_probs=77.4
Q ss_pred CCCCCCHHHHHHHHHHHHhhCCCCccccccccccCccCCCCCHHhHHHHHHhhccCchhhhcccCCCCCCCCCCCCCCCC
Q 024081 4 PKQKWTAEEEEALRAGVAKHGTGKWKNIQRDPEFNPFLFSRSNIDLKDKWRNMSVSAPREKSRTLKPKAGSDAPAVPLST 83 (272)
Q Consensus 4 ~r~~WT~EEe~~L~~GV~KyG~GkW~~I~~~~~f~~~l~~RT~vdLKDKWRnl~~~~~r~k~~~~~~~~~~~~~~~~~~~ 83 (272)
+|++||+|||+.|+..|.+||.++|..|.+. +..+|++.||++||.|.+.+..+ +++-. +
T Consensus 13 rKg~WTpEEDe~L~~~V~kyG~~nWs~IAk~-----~g~gRT~KQCRERW~NyLdP~Ik--------KgpWT-~------ 72 (459)
T PLN03091 13 RKGLWSPEEDEKLLRHITKYGHGCWSSVPKQ-----AGLQRCGKSCRLRWINYLRPDLK--------RGTFS-Q------ 72 (459)
T ss_pred cCCCCCHHHHHHHHHHHHHhCcCCHHHHhhh-----hccCcCcchHhHHHHhccCCccc--------CCCCC-H------
Confidence 5789999999999999999999999999973 12589999999999999987632 22220 0
Q ss_pred CCCCCCCCccCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHhcCCCCCCCHHHHHHHHHhhcC--CCccHHHHHHHHHHh
Q 024081 84 PQTSALPAAVPIDASADPITDESARSSAPKYNALIFEAISALKEPNGSDVSAILSYIEQRLE--VPPNFRRLLSSRLRR 160 (272)
Q Consensus 84 ~~~~~~~~~~~~~~~~~~~~~~~~~~shp~y~~MI~EAI~~Lker~GSS~~AI~kyIe~~y~--v~~nf~~~L~~~LKr 160 (272)
-=+.+|++.+.. -|.....|++|+..+-+ +...|..+|+..|++
T Consensus 73 -----------------------------EED~lLLeL~k~----~GnKWskIAk~LPGRTDnqIKNRWnslLKKklr~ 118 (459)
T PLN03091 73 -----------------------------QEENLIIELHAV----LGNRWSQIAAQLPGRTDNEIKNLWNSCLKKKLRQ 118 (459)
T ss_pred -----------------------------HHHHHHHHHHHH----hCcchHHHHHhcCCCCHHHHHHHHHHHHHHHHHH
Confidence 126677777765 47789999999977652 334455566666654
No 11
>PLN03212 Transcription repressor MYB5; Provisional
Probab=98.66 E-value=8.1e-08 Score=88.25 Aligned_cols=51 Identities=18% Similarity=0.288 Sum_probs=46.6
Q ss_pred CCCCCCCHHHHHHHHHHHHhhCCCCccccccccccCccCCCCCHHhHHHHHHhhccCc
Q 024081 3 NPKQKWTAEEEEALRAGVAKHGTGKWKNIQRDPEFNPFLFSRSNIDLKDKWRNMSVSA 60 (272)
Q Consensus 3 ~~r~~WT~EEe~~L~~GV~KyG~GkW~~I~~~~~f~~~l~~RT~vdLKDKWRnl~~~~ 60 (272)
-.+.+||.|||+.|+..+.+||. +|..|.. +|++||..+||+||.++++..
T Consensus 76 I~kgpWT~EED~lLlel~~~~Gn-KWs~IAk------~LpGRTDnqIKNRWns~LrK~ 126 (249)
T PLN03212 76 VKRGGITSDEEDLILRLHRLLGN-RWSLIAG------RIPGRTDNEIKNYWNTHLRKK 126 (249)
T ss_pred cccCCCChHHHHHHHHHHHhccc-cHHHHHh------hcCCCCHHHHHHHHHHHHhHH
Confidence 35789999999999999999997 9999998 478999999999999988765
No 12
>KOG0048 consensus Transcription factor, Myb superfamily [Transcription]
Probab=98.64 E-value=3.1e-08 Score=89.97 Aligned_cols=105 Identities=18% Similarity=0.258 Sum_probs=77.2
Q ss_pred CCCCCHHHHHHHHHHHHhhCCCCccccccccccCccCCCCCHHhHHHHHHhhccCchhhhcccCCCCCCCCCCCCCCCCC
Q 024081 5 KQKWTAEEEEALRAGVAKHGTGKWKNIQRDPEFNPFLFSRSNIDLKDKWRNMSVSAPREKSRTLKPKAGSDAPAVPLSTP 84 (272)
Q Consensus 5 r~~WT~EEe~~L~~GV~KyG~GkW~~I~~~~~f~~~l~~RT~vdLKDKWRnl~~~~~r~k~~~~~~~~~~~~~~~~~~~~ 84 (272)
|++||+|||+.|+..|++||.|+|..|.++- + .+|+..+|+-||.|.+++..+ ++..+ +
T Consensus 9 kGpWt~EED~~L~~~V~~~G~~~W~~i~k~~--g---l~R~GKSCRlRW~NyLrP~ik--------rg~fT-~------- 67 (238)
T KOG0048|consen 9 KGPWTQEEDLTQIRSIKSFGKHNGTALPKLA--G---LRRCGKSCRLRWTNYLRPDLK--------RGNFS-D------- 67 (238)
T ss_pred CCCCChHHHHHHHHHHHHhCCCCcchhhhhc--C---CCccchHHHHHhhcccCCCcc--------CCCCC-H-------
Confidence 4999999999999999999999999999962 2 299999999999999999863 34331 1
Q ss_pred CCCCCCCccCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHhcCCCCCCCHHHHHHHHHhhc--CCCccHHHHHHHHHHhhh
Q 024081 85 QTSALPAAVPIDASADPITDESARSSAPKYNALIFEAISALKEPNGSDVSAILSYIEQRL--EVPPNFRRLLSSRLRRLV 162 (272)
Q Consensus 85 ~~~~~~~~~~~~~~~~~~~~~~~~~shp~y~~MI~EAI~~Lker~GSS~~AI~kyIe~~y--~v~~nf~~~L~~~LKrlV 162 (272)
-=+.+|+++=..+..+ ...|++++-.+- .+..-++..|+.+|..+-
T Consensus 68 ----------------------------eEe~~Ii~lH~~~GNr----Ws~IA~~LPGRTDNeIKN~Wnt~lkkkl~~~~ 115 (238)
T KOG0048|consen 68 ----------------------------EEEDLIIKLHALLGNR----WSLIAGRLPGRTDNEVKNHWNTHLKKKLLKMG 115 (238)
T ss_pred ----------------------------HHHHHHHHHHHHHCcH----HHHHHhhCCCcCHHHHHHHHHHHHHHHHHHcC
Confidence 1167888877776554 777777776543 221123566666665553
No 13
>PLN03091 hypothetical protein; Provisional
Probab=98.40 E-value=2.5e-07 Score=90.96 Aligned_cols=53 Identities=21% Similarity=0.364 Sum_probs=47.5
Q ss_pred CCCCCCCHHHHHHHHHHHHhhCCCCccccccccccCccCCCCCHHhHHHHHHhhccCchh
Q 024081 3 NPKQKWTAEEEEALRAGVAKHGTGKWKNIQRDPEFNPFLFSRSNIDLKDKWRNMSVSAPR 62 (272)
Q Consensus 3 ~~r~~WT~EEe~~L~~GV~KyG~GkW~~I~~~~~f~~~l~~RT~vdLKDKWRnl~~~~~r 62 (272)
-.+.+||.|||..|++.+.+||. +|..|.. +|++||..+||+||..++++..|
T Consensus 65 IkKgpWT~EED~lLLeL~k~~Gn-KWskIAk------~LPGRTDnqIKNRWnslLKKklr 117 (459)
T PLN03091 65 LKRGTFSQQEENLIIELHAVLGN-RWSQIAA------QLPGRTDNEIKNLWNSCLKKKLR 117 (459)
T ss_pred ccCCCCCHHHHHHHHHHHHHhCc-chHHHHH------hcCCCCHHHHHHHHHHHHHHHHH
Confidence 35789999999999999999998 9999998 47899999999999998876533
No 14
>KOG0048 consensus Transcription factor, Myb superfamily [Transcription]
Probab=97.87 E-value=9.4e-06 Score=73.81 Aligned_cols=51 Identities=22% Similarity=0.361 Sum_probs=45.6
Q ss_pred CCCCCCCHHHHHHHHHHHHhhCCCCccccccccccCccCCCCCHHhHHHHHHhhccCc
Q 024081 3 NPKQKWTAEEEEALRAGVAKHGTGKWKNIQRDPEFNPFLFSRSNIDLKDKWRNMSVSA 60 (272)
Q Consensus 3 ~~r~~WT~EEe~~L~~GV~KyG~GkW~~I~~~~~f~~~l~~RT~vdLKDKWRnl~~~~ 60 (272)
-+|+.||+|||..|+.+-.+||. +|..|.. +|+|||..++|+-|...+++.
T Consensus 60 ikrg~fT~eEe~~Ii~lH~~~GN-rWs~IA~------~LPGRTDNeIKN~Wnt~lkkk 110 (238)
T KOG0048|consen 60 LKRGNFSDEEEDLIIKLHALLGN-RWSLIAG------RLPGRTDNEVKNHWNTHLKKK 110 (238)
T ss_pred ccCCCCCHHHHHHHHHHHHHHCc-HHHHHHh------hCCCcCHHHHHHHHHHHHHHH
Confidence 36889999999999999999999 9999999 489999999999997666544
No 15
>TIGR01557 myb_SHAQKYF myb-like DNA-binding domain, SHAQKYF class. This model describes a DNA-binding domain restricted to (but common in) plant proteins, many of which also contain a response regulator domain. The domain appears related to the Myb-like DNA-binding domain described by Pfam model pfam00249. It is distinguished in part by a well-conserved motif SH[AL]QKY[RF] at the C-terminal end of the motif.
Probab=97.81 E-value=3.4e-05 Score=56.29 Aligned_cols=48 Identities=19% Similarity=0.380 Sum_probs=39.7
Q ss_pred CCCCCCCHHHHHHHHHHHHhhCCCCc---cccccccccCccCCCC-CHHhHHHHHHh
Q 024081 3 NPKQKWTAEEEEALRAGVAKHGTGKW---KNIQRDPEFNPFLFSR-SNIDLKDKWRN 55 (272)
Q Consensus 3 ~~r~~WT~EEe~~L~~GV~KyG~GkW---~~I~~~~~f~~~l~~R-T~vdLKDKWRn 55 (272)
.+|..||+||...++.||+.||.|+| +.|+... -..| |..+++.....
T Consensus 1 k~r~~WT~eeh~~Fl~ai~~~G~g~~a~pk~I~~~~-----~~~~lT~~qV~SH~QK 52 (57)
T TIGR01557 1 KPRVVWTEDLHDRFLQAVQKLGGPDWATPKRILELM-----VVDGLTRDQVASHLQK 52 (57)
T ss_pred CCCCCCCHHHHHHHHHHHHHhCCCcccchHHHHHHc-----CCCCCCHHHHHHHHHH
Confidence 47889999999999999999999999 9998742 1245 99999876543
No 16
>KOG0051 consensus RNA polymerase I termination factor, Myb superfamily [Transcription]
Probab=97.47 E-value=6.1e-05 Score=76.86 Aligned_cols=50 Identities=38% Similarity=0.780 Sum_probs=46.6
Q ss_pred CCCCCCHHHHHHHHHHHHhhCCCCccccccccccCccCCCCCHHhHHHHHHhhccCch
Q 024081 4 PKQKWTAEEEEALRAGVAKHGTGKWKNIQRDPEFNPFLFSRSNIDLKDKWRNMSVSAP 61 (272)
Q Consensus 4 ~r~~WT~EEe~~L~~GV~KyG~GkW~~I~~~~~f~~~l~~RT~vdLKDKWRnl~~~~~ 61 (272)
.|+.||+||++.|...|..||. .|..|-+ .-+|.|.+|+|+||++...++
T Consensus 383 ~rg~wt~ee~eeL~~l~~~~g~-~W~~Ig~-------~lgr~P~~crd~wr~~~~~g~ 432 (607)
T KOG0051|consen 383 KRGKWTPEEEEELKKLVVEHGN-DWKEIGK-------ALGRMPMDCRDRWRQYVKCGS 432 (607)
T ss_pred ccCCCCcchHHHHHHHHHHhcc-cHHHHHH-------HHccCcHHHHHHHHHhhcccc
Confidence 6889999999999999999998 9999998 369999999999999999874
No 17
>KOG0049 consensus Transcription factor, Myb superfamily [Transcription]
Probab=97.35 E-value=0.00016 Score=74.31 Aligned_cols=51 Identities=20% Similarity=0.490 Sum_probs=45.7
Q ss_pred CCCCCCCCHHHHHHHHHHHHhhCCCCccccccccccCccCCCCCHHhHHHHHHhhcc
Q 024081 2 GNPKQKWTAEEEEALRAGVAKHGTGKWKNIQRDPEFNPFLFSRSNIDLKDKWRNMSV 58 (272)
Q Consensus 2 g~~r~~WT~EEe~~L~~GV~KyG~GkW~~I~~~~~f~~~l~~RT~vdLKDKWRnl~~ 58 (272)
|-+.++||.+||..|+.+|.+||.--|.+|... |++|+..||++||.|.+.
T Consensus 357 sikhg~wt~~ED~~L~~AV~~Yg~kdw~k~R~~------vPnRSdsQcR~RY~nvL~ 407 (939)
T KOG0049|consen 357 SVKHGRWTDQEDVLLVCAVSRYGAKDWAKVRQA------VPNRSDSQCRERYTNVLN 407 (939)
T ss_pred cccCCCCCCHHHHHHHHHHHHhCccchhhHHHh------cCCccHHHHHHHHHHHHH
Confidence 446789999999999999999999999999983 689999999999977654
No 18
>KOG0457 consensus Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=97.10 E-value=0.00033 Score=69.03 Aligned_cols=49 Identities=24% Similarity=0.491 Sum_probs=44.2
Q ss_pred CCCCHHHHHHHHHHHHhhCCCCccccccccccCccCCCCCHHhHHHHHHhhccCc
Q 024081 6 QKWTAEEEEALRAGVAKHGTGKWKNIQRDPEFNPFLFSRSNIDLKDKWRNMSVSA 60 (272)
Q Consensus 6 ~~WT~EEe~~L~~GV~KyG~GkW~~I~~~~~f~~~l~~RT~vdLKDKWRnl~~~~ 60 (272)
--||.+||-.|++++++||-|+|..|.+. .-.+|.-+||+.|.++...+
T Consensus 73 ~~WtadEEilLLea~~t~G~GNW~dIA~h------IGtKtkeeck~hy~k~fv~s 121 (438)
T KOG0457|consen 73 PSWTADEEILLLEAAETYGFGNWQDIADH------IGTKTKEECKEHYLKHFVNS 121 (438)
T ss_pred CCCChHHHHHHHHHHHHhCCCcHHHHHHH------HcccchHHHHHHHHHHHhcC
Confidence 35999999999999999999999999984 34799999999999988765
No 19
>PF13837 Myb_DNA-bind_4: Myb/SANT-like DNA-binding domain; PDB: 2EBI_A 2JMW_A.
Probab=96.94 E-value=0.00019 Score=54.62 Aligned_cols=54 Identities=22% Similarity=0.500 Sum_probs=36.1
Q ss_pred CCCCCHHHHHHHHHHHHh------hCC-----C--CccccccccccCccCCCCCHHhHHHHHHhhccCc
Q 024081 5 KQKWTAEEEEALRAGVAK------HGT-----G--KWKNIQRDPEFNPFLFSRSNIDLKDKWRNMSVSA 60 (272)
Q Consensus 5 r~~WT~EEe~~L~~GV~K------yG~-----G--kW~~I~~~~~f~~~l~~RT~vdLKDKWRnl~~~~ 60 (272)
|..||.+|+..|++.+.. ++. + -|..|... +...-..||+.||++||.||.+.-
T Consensus 1 R~~Wt~~et~~Li~~~~~~~~~~~~~~~~~~~~~~~w~~Ia~~--l~~~G~~rt~~qc~~Kw~~L~~~Y 67 (90)
T PF13837_consen 1 RRNWTDEETKLLIELWKENLMELRFDNGGKKRNKKVWKEIAEE--LAEHGYNRTPEQCRNKWKNLKKKY 67 (90)
T ss_dssp --SS-HHHHHHHHHHHHH--HHHHHHH--SS--HHHHHHHHHH--HHHHC----HHHHHHHHHHHHHHH
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHhhhccccchHHHHHHHHH--HHHcCCCCCHHHHHHHHHHHHHHH
Confidence 578999999999999887 221 2 59999874 222224899999999999998765
No 20
>KOG0049 consensus Transcription factor, Myb superfamily [Transcription]
Probab=96.88 E-value=0.00043 Score=71.31 Aligned_cols=49 Identities=22% Similarity=0.426 Sum_probs=42.1
Q ss_pred CCCCCCCHHHHHHHHHHHHhhCCCCccccccccccCccCCCCCHHhHHHHHHhhc
Q 024081 3 NPKQKWTAEEEEALRAGVAKHGTGKWKNIQRDPEFNPFLFSRSNIDLKDKWRNMS 57 (272)
Q Consensus 3 ~~r~~WT~EEe~~L~~GV~KyG~GkW~~I~~~~~f~~~l~~RT~vdLKDKWRnl~ 57 (272)
.++..||-.||+.|+..|++||.|+|.+|.. +|++||..|+..+-+.+.
T Consensus 410 ~K~~rW~l~edeqL~~~V~~YG~g~WakcA~------~Lp~~t~~q~~rrR~R~~ 458 (939)
T KOG0049|consen 410 AKVERWTLVEDEQLLYAVKVYGKGNWAKCAM------LLPKKTSRQLRRRRLRLI 458 (939)
T ss_pred hccCceeecchHHHHHHHHHHccchHHHHHH------HccccchhHHHHHHHHHH
Confidence 4678999999999999999999999999997 589999987776654443
No 21
>PF09111 SLIDE: SLIDE; InterPro: IPR015195 The SLIDE domain adopts a secondary structure comprising a main core of three alpha-helices. It has a role in DNA binding, contacting DNA target sites similar to c-Myb (IPR014778 from INTERPRO) repeats or homeodomains []. ; GO: 0003676 nucleic acid binding, 0005524 ATP binding, 0016818 hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides, 0006338 chromatin remodeling, 0005634 nucleus; PDB: 2NOG_A 2Y9Y_A 2Y9Z_A 1OFC_X.
Probab=96.41 E-value=0.0015 Score=54.14 Aligned_cols=57 Identities=28% Similarity=0.517 Sum_probs=45.0
Q ss_pred CCCCCCCHHHHHHHHHHHHhhCC---CCccccccc----c--ccCccCCCCCHHhHHHHHHhhccC
Q 024081 3 NPKQKWTAEEEEALRAGVAKHGT---GKWKNIQRD----P--EFNPFLFSRSNIDLKDKWRNMSVS 59 (272)
Q Consensus 3 ~~r~~WT~EEe~~L~~GV~KyG~---GkW~~I~~~----~--~f~~~l~~RT~vdLKDKWRnl~~~ 59 (272)
..+..||.+||..|+-.+.+||- |.|..|..+ | .|+-||.+||+.+|..|-..|...
T Consensus 47 ~~~k~yseeEDRfLl~~~~~~G~~~~~~~e~Ik~~Ir~~p~FrFDwf~kSRt~~el~rR~~tLi~~ 112 (118)
T PF09111_consen 47 NKKKVYSEEEDRFLLCMLYKYGYDAEGNWEKIKQEIRESPLFRFDWFFKSRTPQELQRRCNTLIKL 112 (118)
T ss_dssp SS-SSS-HHHHHHHHHHHHHHTTTSTTHHHHHHHHHHH-CGGCT-HHHHTS-HHHHHHHHHHHHHH
T ss_pred CCCCCcCcHHHHHHHHHHHHhCCCCCchHHHHHHHHHhCCCcccchhcccCCHHHHHHHHHHHHHH
Confidence 45788999999999999999999 999887653 3 565577999999999998887654
No 22
>PF13873 Myb_DNA-bind_5: Myb/SANT-like DNA-binding domain
Probab=95.91 E-value=0.0049 Score=46.19 Aligned_cols=54 Identities=35% Similarity=0.551 Sum_probs=43.8
Q ss_pred CCCCCHHHHHHHHHHHHhh-----CC-----------CCccccccccccCccC-CCCCHHhHHHHHHhhccCc
Q 024081 5 KQKWTAEEEEALRAGVAKH-----GT-----------GKWKNIQRDPEFNPFL-FSRSNIDLKDKWRNMSVSA 60 (272)
Q Consensus 5 r~~WT~EEe~~L~~GV~Ky-----G~-----------GkW~~I~~~~~f~~~l-~~RT~vdLKDKWRnl~~~~ 60 (272)
...||.+|...|++.|++| |. .-|..|... |+.+. ..||..+|+.+|.||....
T Consensus 2 ~~~fs~~E~~~Lv~~v~~~~~il~~k~~~~~~~~~k~~~W~~I~~~--lN~~~~~~Rs~~~lkkkW~nlk~~~ 72 (78)
T PF13873_consen 2 KPNFSEEEKEILVELVEKHKDILENKFSDSVSNKEKRKAWEEIAEE--LNALGPGKRSWKQLKKKWKNLKSKA 72 (78)
T ss_pred CCCCCHHHHHHHHHHHHHhHHHHhcccccHHHHHHHHHHHHHHHHH--HHhcCCCCCCHHHHHHHHHHHHHHH
Confidence 4679999999999999998 31 469999985 44433 3899999999999997654
No 23
>KOG1279 consensus Chromatin remodeling factor subunit and related transcription factors [Chromatin structure and dynamics]
Probab=95.21 E-value=0.019 Score=58.20 Aligned_cols=49 Identities=16% Similarity=0.375 Sum_probs=43.3
Q ss_pred CCCCCCHHHHHHHHHHHHhhCCCCccccccccccCccCCCCCHHhHHHHHHhhccC
Q 024081 4 PKQKWTAEEEEALRAGVAKHGTGKWKNIQRDPEFNPFLFSRSNIDLKDKWRNMSVS 59 (272)
Q Consensus 4 ~r~~WT~EEe~~L~~GV~KyG~GkW~~I~~~~~f~~~l~~RT~vdLKDKWRnl~~~ 59 (272)
.+..||.+|.-.|++||++||. .|.+|..+ ..+||.-||-.|+..|=..
T Consensus 252 ~~~~WT~qE~lLLLE~ie~y~d-dW~kVa~h------Vg~ks~eqCI~kFL~LPie 300 (506)
T KOG1279|consen 252 ARPNWTEQETLLLLEAIEMYGD-DWNKVADH------VGTKSQEQCILKFLRLPIE 300 (506)
T ss_pred CCCCccHHHHHHHHHHHHHhcc-cHHHHHhc------cCCCCHHHHHHHHHhcCcc
Confidence 3568999999999999999999 99999985 3599999999999887544
No 24
>PF13325 MCRS_N: N-terminal region of micro-spherule protein
Probab=95.05 E-value=0.014 Score=52.63 Aligned_cols=56 Identities=23% Similarity=0.337 Sum_probs=46.3
Q ss_pred CCCCCCHHHHHHHHHHHHhhC--CCCccccccccccCccCCCCCHHhHHHHHHhhccCc
Q 024081 4 PKQKWTAEEEEALRAGVAKHG--TGKWKNIQRDPEFNPFLFSRSNIDLKDKWRNMSVSA 60 (272)
Q Consensus 4 ~r~~WT~EEe~~L~~GV~KyG--~GkW~~I~~~~~f~~~l~~RT~vdLKDKWRnl~~~~ 60 (272)
.+.+||.+||+.|........ ...+.+|+.++. ..|...||+.+|.+.|+.|.+..
T Consensus 72 ~kalfS~~EE~lL~~v~s~~~p~le~Fq~LL~~n~-~vFh~sRTak~L~~HW~lmkqy~ 129 (199)
T PF13325_consen 72 SKALFSKEEEQLLGTVASSSQPSLETFQELLDKNR-SVFHPSRTAKSLQDHWRLMKQYH 129 (199)
T ss_pred ccCCCCHHHHHHHHhhhhccCCcHHHHHHHHHhCh-hhhccccCHHHHHHHHHHHHHhc
Confidence 578999999999999877764 468999999753 22557899999999999998776
No 25
>KOG0050 consensus mRNA splicing protein CDC5 (Myb superfamily) [RNA processing and modification; Cell cycle control, cell division, chromosome partitioning]
Probab=95.00 E-value=0.0094 Score=60.26 Aligned_cols=49 Identities=29% Similarity=0.562 Sum_probs=43.8
Q ss_pred CCCCHHHHHHHHHHHHhhCCCCccccccccccCccCCCCCHHhHHHHHHhhccCc
Q 024081 6 QKWTAEEEEALRAGVAKHGTGKWKNIQRDPEFNPFLFSRSNIDLKDKWRNMSVSA 60 (272)
Q Consensus 6 ~~WT~EEe~~L~~GV~KyG~GkW~~I~~~~~f~~~l~~RT~vdLKDKWRnl~~~~ 60 (272)
.-|+.-||+.|..+|.+||...|+.|.. .++.-|..+|+.+|--...+.
T Consensus 8 gvwrntEdeilkaav~kyg~nqws~i~s------ll~~kt~rqC~~rw~e~ldp~ 56 (617)
T KOG0050|consen 8 GVWRNTEDEVLKAAVMKYGKNQWSRIAS------LLNRKTARQCKARWEEWLDPA 56 (617)
T ss_pred ceecccHHHHHHHHHHHcchHHHHHHHH------HHhhcchhHHHHHHHHHhCHH
Confidence 4699999999999999999999999998 367889999999998766655
No 26
>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional
Probab=94.82 E-value=0.026 Score=61.57 Aligned_cols=60 Identities=20% Similarity=0.301 Sum_probs=50.6
Q ss_pred CCCCCCHHHHHHHHHHHHhhCCCCccccc------cccccCccCCCCCHHhHHHHHHhhccCchhh
Q 024081 4 PKQKWTAEEEEALRAGVAKHGTGKWKNIQ------RDPEFNPFLFSRSNIDLKDKWRNMSVSAPRE 63 (272)
Q Consensus 4 ~r~~WT~EEe~~L~~GV~KyG~GkW~~I~------~~~~f~~~l~~RT~vdLKDKWRnl~~~~~r~ 63 (272)
.++.||.|||..|+-.+.+||-|+|..|. -.+.|+-||..||+..|..|-..|.+.-.|+
T Consensus 925 ~~~~~~~~~d~~~~~~~~~~g~~~~~~~~~~i~~~~~f~fd~~~~srt~~~~~~r~~~l~~~~~~e 990 (1033)
T PLN03142 925 KGKLYNEECDRFMLCMVHKLGYGNWDELKAAFRTSPLFRFDWFVKSRTPQELARRCDTLIRLIEKE 990 (1033)
T ss_pred CCCcCCHHHHHHHHHHHHHhccchHHHHHHHHHhCCceeeehhhccCCHHHHHHHHHHHHHHHHHH
Confidence 45569999999999999999999999983 2346777889999999999999888766444
No 27
>COG5147 REB1 Myb superfamily proteins, including transcription factors and mRNA splicing factors [Transcription / RNA processing and modification / Cell division and chromosome partitioning]
Probab=94.57 E-value=0.0093 Score=60.41 Aligned_cols=49 Identities=35% Similarity=0.677 Sum_probs=45.4
Q ss_pred CCCCCCHHHHHHHHHHHHhhCCCCccccccccccCccCCCCCHHhHHHHHHhhccCc
Q 024081 4 PKQKWTAEEEEALRAGVAKHGTGKWKNIQRDPEFNPFLFSRSNIDLKDKWRNMSVSA 60 (272)
Q Consensus 4 ~r~~WT~EEe~~L~~GV~KyG~GkW~~I~~~~~f~~~l~~RT~vdLKDKWRnl~~~~ 60 (272)
.++.||.||+..|...+.++|. .|..|-.. .+|-+.+|+|+||+..+.+
T Consensus 290 ~~~~wt~e~~~eL~~~~~~~~~-~w~~ig~~-------~~rmp~~crd~wr~~~~~g 338 (512)
T COG5147 290 QRGKWTKEEEQELAKLVVEHGG-SWTEIGKL-------LGRMPNDCRDRWRDYVKCG 338 (512)
T ss_pred hhccCccccccccccccccccc-hhhHhhhh-------hccCcHHHHHHHhhhcccc
Confidence 4789999999999999999998 99999984 4899999999999999987
No 28
>PF08074 CHDCT2: CHDCT2 (NUC038) domain; InterPro: IPR012957 The CHDCT2 C-terminal domain is found in PHD/RING fingers and chromo domain-associated CHD-like helicases [].; GO: 0003677 DNA binding, 0005524 ATP binding, 0008270 zinc ion binding, 0016818 hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=94.24 E-value=0.026 Score=49.60 Aligned_cols=47 Identities=34% Similarity=0.784 Sum_probs=37.9
Q ss_pred CCCCHHHHHHHHHHHHhhCCCCccccccccccCccCC--CC------CHHhHHHHH
Q 024081 6 QKWTAEEEEALRAGVAKHGTGKWKNIQRDPEFNPFLF--SR------SNIDLKDKW 53 (272)
Q Consensus 6 ~~WT~EEe~~L~~GV~KyG~GkW~~I~~~~~f~~~l~--~R------T~vdLKDKW 53 (272)
.-|-..-|-+|+.||.+||-|.|..|+.||.|. +++ =+ +.-++|+||
T Consensus 4 ~iw~r~hdywll~gi~~hgy~rwqdi~nd~~f~-IiNEPFk~e~~kgnfle~KNkF 58 (173)
T PF08074_consen 4 EIWHRRHDYWLLAGIVKHGYGRWQDIQNDPRFA-IINEPFKTESQKGNFLEMKNKF 58 (173)
T ss_pred hhhhhhhhHHHHhHHhhccchhHHHHhcCCcee-eecccccccccccchHHHHHHH
Confidence 358888999999999999999999999999886 331 12 335888887
No 29
>COG5259 RSC8 RSC chromatin remodeling complex subunit RSC8 [Chromatin structure and dynamics / Transcription]
Probab=93.53 E-value=0.056 Score=54.28 Aligned_cols=45 Identities=16% Similarity=0.401 Sum_probs=40.5
Q ss_pred CCCCHHHHHHHHHHHHhhCCCCccccccccccCccCCCCCHHhHHHHHHhhc
Q 024081 6 QKWTAEEEEALRAGVAKHGTGKWKNIQRDPEFNPFLFSRSNIDLKDKWRNMS 57 (272)
Q Consensus 6 ~~WT~EEe~~L~~GV~KyG~GkW~~I~~~~~f~~~l~~RT~vdLKDKWRnl~ 57 (272)
..||.+|.-.|++||+.||. .|.+|..+ ..++|.-||--|+-+|=
T Consensus 280 k~WS~qE~~LLLEGIe~ygD-dW~kVA~H------VgtKt~EqCIl~FL~LP 324 (531)
T COG5259 280 KNWSRQELLLLLEGIEMYGD-DWDKVARH------VGTKTKEQCILHFLQLP 324 (531)
T ss_pred ccccHHHHHHHHHHHHHhhh-hHHHHHHH------hCCCCHHHHHHHHHcCC
Confidence 48999999999999999999 99999985 46999999999987663
No 30
>PF00250 Fork_head: Fork head domain; InterPro: IPR001766 The fork head protein of Drosophila melanogaster, a transcription factor that promotes terminal rather than segmental development, contains neither homeodomains nor zinc-fingers characteristic of other transcription factors []. Instead, it contains a distinct type of DNA-binding region, containing around 100 amino acids, which has since been identified in a number of transcription factors (including D. melanogaster FD1-5, mammalian HNF-3, human HTLF, Saccharomyces cerevisiae HCM1, etc.). This is referred to as the fork head domain but is also known as a 'winged helix' [, , ]. The fork head domain binds B-DNA as a monomer [], but shows no similarity to previously identified DNA-binding motifs. Although the domain is found in several different transcription factors, a common function is their involvement in early developmental decisions of cell fates during embryogenesis [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2UZK_A 2K86_A 1JXS_A 2C6Y_A 2A3S_A 2D2W_A 2KIU_A 1VTN_C 2A07_J 2AS5_F ....
Probab=92.78 E-value=0.2 Score=40.02 Aligned_cols=57 Identities=21% Similarity=0.314 Sum_probs=42.3
Q ss_pred CCCHHHHHHHHHHhcCCCCCCCHHHHHHHHHhhc----CCCccHHHHHHHHHHhhhccCceeeec
Q 024081 111 APKYNALIFEAISALKEPNGSDVSAILSYIEQRL----EVPPNFRRLLSSRLRRLVAQEKLEKVQ 171 (272)
Q Consensus 111 hp~y~~MI~EAI~~Lker~GSS~~AI~kyIe~~y----~v~~nf~~~L~~~LKrlV~~GkLvkvK 171 (272)
.-+|..||..||.+ -..++.+..-|.+||+.+| ..+..++..|++.|- .+.-|+++.
T Consensus 3 p~sY~~LI~~Ai~~-sp~~~Ltl~eIy~~i~~~~pyyr~~~~~WknSIRHnLS---~~~~F~kv~ 63 (96)
T PF00250_consen 3 PYSYATLIAMAILS-SPDKRLTLSEIYEWIEENFPYYRDASKGWKNSIRHNLS---LNKCFVKVP 63 (96)
T ss_dssp SS-HHHHHHHHHHT-STTSEBEHHHHHHHHHHHCGHHHCTHCHHHHHHHHHHH---HSTTEEEES
T ss_pred CCcHHHHHHHHHHh-CCCCCccHHHHHHHHHHhhccccccchhhhhHHhhhcc---ccceeeecC
Confidence 34799999999998 3345689999999999998 235667777777774 445666654
No 31
>PF10264 Stork_head: Winged helix Storkhead-box1 domain; InterPro: IPR019391 In humans the Storkhead-box protein controls polyploidization of extravillus trophoblast and is implicated in pre-eclampsia []. This entry represents the conserved N-terminal winged-helix domain, which is likely to bind DNA.
Probab=92.60 E-value=0.54 Score=36.78 Aligned_cols=66 Identities=11% Similarity=0.140 Sum_probs=55.6
Q ss_pred CCHHHHHHHHHHhcCC-CCCCCHHHHHHHHHhhc-CCCccHHHHHHHHHHhhhccCceeeeccccccC
Q 024081 112 PKYNALIFEAISALKE-PNGSDVSAILSYIEQRL-EVPPNFRRLLSSRLRRLVAQEKLEKVQNCFKVK 177 (272)
Q Consensus 112 p~y~~MI~EAI~~Lke-r~GSS~~AI~kyIe~~y-~v~~nf~~~L~~~LKrlV~~GkLvkvK~sykl~ 177 (272)
-++.+.|..+|..|+- ....+..+|..++..+| ++..--...|..+|-.|+..|+|..+.+-|.|-
T Consensus 10 iPL~EvlC~~I~dln~~~~~at~E~l~~~L~~~yp~i~~Ps~e~l~~~L~~Li~erkIY~tg~GYfiv 77 (80)
T PF10264_consen 10 IPLPEVLCWVISDLNAAGQPATQETLREHLRKHYPGIAIPSQEVLYNTLGTLIKERKIYHTGEGYFIV 77 (80)
T ss_pred eeHHHHHHHHHHHHhccCCcchHHHHHHHHHHhCCCCCCCCHHHHHHHHHHHHHcCceeeCCCceEee
Confidence 4689999999999976 45579999999999999 442223688999999999999999998888774
No 32
>COG5114 Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=92.59 E-value=0.073 Score=51.39 Aligned_cols=46 Identities=28% Similarity=0.481 Sum_probs=41.3
Q ss_pred CCCHHHHHHHHHHHHhhCCCCccccccccccCccCCCCCHHhHHHHHHhhcc
Q 024081 7 KWTAEEEEALRAGVAKHGTGKWKNIQRDPEFNPFLFSRSNIDLKDKWRNMSV 58 (272)
Q Consensus 7 ~WT~EEe~~L~~GV~KyG~GkW~~I~~~~~f~~~l~~RT~vdLKDKWRnl~~ 58 (272)
-|+..||-.|+++.+..|.|+|..|... .-.|+..+||+.|-.|..
T Consensus 65 ~WgadEEllli~~~~TlGlGNW~dIady------iGsr~kee~k~HylK~y~ 110 (432)
T COG5114 65 GWGADEELLLIECLDTLGLGNWEDIADY------IGSRAKEEIKSHYLKMYD 110 (432)
T ss_pred CcCchHHHHHHHHHHhcCCCcHHHHHHH------HhhhhhHHHHHHHHHHHh
Confidence 5999999999999999999999999973 458999999999977655
No 33
>cd00059 FH Forkhead (FH), also known as a "winged helix". FH is named for the Drosophila fork head protein, a transcription factor which promotes terminal rather than segmental development. This family of transcription factor domains, which bind to B-DNA as monomers, are also found in the Hepatocyte nuclear factor (HNF) proteins, which provide tissue-specific gene regulation. The structure contains 2 flexible loops or "wings" in the C-terminal region, hence the term winged helix.
Probab=92.47 E-value=0.13 Score=39.69 Aligned_cols=47 Identities=23% Similarity=0.369 Sum_probs=34.9
Q ss_pred CCCHHHHHHHHHHhcCCCCCCCHHHHHHHHHhhcC----CCccHHHHHHHHH
Q 024081 111 APKYNALIFEAISALKEPNGSDVSAILSYIEQRLE----VPPNFRRLLSSRL 158 (272)
Q Consensus 111 hp~y~~MI~EAI~~Lker~GSS~~AI~kyIe~~y~----v~~nf~~~L~~~L 158 (272)
.-+|..||..||.... .++.+..-|.+||+++|. -+..++..+++.|
T Consensus 3 ~~sY~~LI~~Ai~~sp-~~~lTL~eIy~~I~~~~pyyr~~~~gWknSIRHnL 53 (78)
T cd00059 3 PYSYSALIAMAIQSSP-EKRLTLSEIYKWISDNFPYFRDAPAGWQNSIRHNL 53 (78)
T ss_pred CCCHHHHHHHHHHhCC-CCCeeHHHHHHHHHHhCCccccCCCCCccceeEec
Confidence 4579999999999955 566999999999999982 2344444444433
No 34
>PF14338 Mrr_N: Mrr N-terminal domain
Probab=92.14 E-value=0.4 Score=37.25 Aligned_cols=66 Identities=17% Similarity=0.325 Sum_probs=55.5
Q ss_pred CHHHHHHHHHHhcCC-CCCCCHHHHHHHHHhhcCCC--------------ccHHHHHHHHHHhhhccCceeeec-ccccc
Q 024081 113 KYNALIFEAISALKE-PNGSDVSAILSYIEQRLEVP--------------PNFRRLLSSRLRRLVAQEKLEKVQ-NCFKV 176 (272)
Q Consensus 113 ~y~~MI~EAI~~Lke-r~GSS~~AI~kyIe~~y~v~--------------~nf~~~L~~~LKrlV~~GkLvkvK-~sykl 176 (272)
+|++|+.-.|..|++ .+..++..|...|.+++++. +.|...++=++..|+..|-|..++ |.|+|
T Consensus 1 ~~~~~~~piL~~L~~~g~~~~~~ei~~~v~~~~~ls~e~~~~~~~sg~~~~~~~~ri~Wa~~~L~~aGli~~~~rG~~~i 80 (92)
T PF14338_consen 1 TYDELMPPILEALKDLGGSASRKEIYERVAERFGLSDEERNERLPSGQGYSRFKNRIRWARSYLKKAGLIERPKRGIWRI 80 (92)
T ss_pred CHHHHHHHHHHHHHHcCCCcCHHHHHHHHHHHhCCCHHHHHHHcccCCcchhHHHhHHHHHHHHHHCCCccCCCCCceEE
Confidence 589999999999999 66789999999999987432 147888889999999999999965 68999
Q ss_pred CC
Q 024081 177 KE 178 (272)
Q Consensus 177 ~~ 178 (272)
++
T Consensus 81 T~ 82 (92)
T PF14338_consen 81 TE 82 (92)
T ss_pred CH
Confidence 75
No 35
>COG5147 REB1 Myb superfamily proteins, including transcription factors and mRNA splicing factors [Transcription / RNA processing and modification / Cell division and chromosome partitioning]
Probab=91.27 E-value=0.074 Score=54.04 Aligned_cols=50 Identities=26% Similarity=0.501 Sum_probs=43.0
Q ss_pred CCCCCCHHHHHHHHHHHHhhCCCCccccccccccCccCCCCCHHhHHHHHHhhccC
Q 024081 4 PKQKWTAEEEEALRAGVAKHGTGKWKNIQRDPEFNPFLFSRSNIDLKDKWRNMSVS 59 (272)
Q Consensus 4 ~r~~WT~EEe~~L~~GV~KyG~GkW~~I~~~~~f~~~l~~RT~vdLKDKWRnl~~~ 59 (272)
..+.|+..||+.|..+|++||+-+|..|... |..|++.||+.+|-+...+
T Consensus 19 k~gsw~~~EDe~l~~~vk~l~~nnws~vas~------~~~~~~kq~~~rw~~~lnp 68 (512)
T COG5147 19 KGGSWKRTEDEDLKALVKKLGPNNWSKVASL------LISSTGKQSSNRWNNHLNP 68 (512)
T ss_pred cCCCCCCcchhHHHHHHhhcccccHHHHHHH------hcccccccccchhhhhhch
Confidence 4568999999999999999999999999984 4569999999999555444
No 36
>KOG4282 consensus Transcription factor GT-2 and related proteins, contains trihelix DNA-binding/SANT domain [Transcription]
Probab=90.57 E-value=0.22 Score=47.32 Aligned_cols=62 Identities=24% Similarity=0.415 Sum_probs=47.5
Q ss_pred CCCCCHHHHHHHHHHHHh----hCCCC-----ccccccccccCccCCCCCHHhHHHHHHhhccCchhhhcccC
Q 024081 5 KQKWTAEEEEALRAGVAK----HGTGK-----WKNIQRDPEFNPFLFSRSNIDLKDKWRNMSVSAPREKSRTL 68 (272)
Q Consensus 5 r~~WT~EEe~~L~~GV~K----yG~Gk-----W~~I~~~~~f~~~l~~RT~vdLKDKWRnl~~~~~r~k~~~~ 68 (272)
-..|+.+|...|+....+ ++.|+ |..|... +...-..||+.+|+.||.||.+.-.++|.+..
T Consensus 54 ~~~Ws~~et~~Li~~~~~~~~~~~~~~~k~~~We~va~k--~~~~g~~rs~~qck~K~~nl~k~Yk~~k~~~~ 124 (345)
T KOG4282|consen 54 EPRWSEEETLTLIEIRGEMDVALRRGKLKGPLWEEVARK--MAELGYPRSPKQCKAKIENLKKKYKKEKAKKE 124 (345)
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHhhhhcccHHHHHHHH--HHHhCCCCCHHHHHHHHHHHHHHHHHHhcccC
Confidence 378999999999987765 34455 9999882 22233589999999999999998766666544
No 37
>smart00339 FH FORKHEAD. FORKHEAD, also known as a "winged helix"
Probab=89.82 E-value=0.41 Score=37.70 Aligned_cols=46 Identities=24% Similarity=0.277 Sum_probs=33.9
Q ss_pred CCHHHHHHHHHHhcCCCCCCCHHHHHHHHHhhcC----CCccHHHHHHHHH
Q 024081 112 PKYNALIFEAISALKEPNGSDVSAILSYIEQRLE----VPPNFRRLLSSRL 158 (272)
Q Consensus 112 p~y~~MI~EAI~~Lker~GSS~~AI~kyIe~~y~----v~~nf~~~L~~~L 158 (272)
-+|..||..||... ..++.+...|.+||+++|. -+.+++..+++.|
T Consensus 4 ~sY~~lI~~ai~~s-p~~~ltl~~Iy~~I~~~~pyy~~~~~~WknSIRHnL 53 (89)
T smart00339 4 YSYIALIAMAILSS-PDKRLTLSEIYKWIEDNFPYYRENRAGWQNSIRHNL 53 (89)
T ss_pred CCHHHHHHHHHHhC-CCCCeeHHHHHHHHHHhCchhhcCcccccccccccc
Confidence 46999999999995 4567899999999999982 2344444444433
No 38
>KOG0384 consensus Chromodomain-helicase DNA-binding protein [Transcription]
Probab=89.24 E-value=0.18 Score=55.84 Aligned_cols=52 Identities=25% Similarity=0.537 Sum_probs=38.5
Q ss_pred CCCCHHHHHHHHHHHHhhCCCCccccccccccCc---cC---CCCCHHhHHHHHHhhc
Q 024081 6 QKWTAEEEEALRAGVAKHGTGKWKNIQRDPEFNP---FL---FSRSNIDLKDKWRNMS 57 (272)
Q Consensus 6 ~~WT~EEe~~L~~GV~KyG~GkW~~I~~~~~f~~---~l---~~RT~vdLKDKWRnl~ 57 (272)
--|..++|..|+-||-+||-|+|..|..||.+.- +| ..=+..+|.-|-.-++
T Consensus 1134 ~~W~~e~Ds~LLiGI~khGygswe~Ir~Dp~L~l~dKi~~~e~~P~a~~L~~R~~yLl 1191 (1373)
T KOG0384|consen 1134 CDWGSEDDSMLLIGIFKHGYGSWEAIRLDPDLGLTDKIFLVETVPQAKHLQRRADYLL 1191 (1373)
T ss_pred cCCCchhhhhHhhhhhhcccccHHHhccCccccchhhhcccccCCchHHHHHHHHHHH
Confidence 3599999999999999999999999999997641 11 1233556666654443
No 39
>PF08914 Myb_DNA-bind_2: Rap1 Myb domain; InterPro: IPR015010 Rap1 Myb adopts a canonical three-helix bundle tertiary structure, with the second and third helices forming a helix-turn-helix variant motif. The function is unclear but it may either interact with DNA via an adaptor protein or it may be only involved in protein-protein interactions []. ; PDB: 1FEX_A.
Probab=87.87 E-value=0.64 Score=34.77 Aligned_cols=50 Identities=18% Similarity=0.322 Sum_probs=29.5
Q ss_pred CCCCCHHHHHHHHHHHHhhCC------C--CccccccccccCccCCCCCHHhHHHHHHhhccC
Q 024081 5 KQKWTAEEEEALRAGVAKHGT------G--KWKNIQRDPEFNPFLFSRSNIDLKDKWRNMSVS 59 (272)
Q Consensus 5 r~~WT~EEe~~L~~GV~KyG~------G--kW~~I~~~~~f~~~l~~RT~vdLKDKWRnl~~~ 59 (272)
|.++|.|||.+|++-|..+.. | =|..+.... ...+|--.++|||+.-+..
T Consensus 2 R~~fT~edD~~l~~~v~~~~~~~~~~~Gn~iwk~le~~~-----~t~HtwQSwR~Ry~K~L~~ 59 (65)
T PF08914_consen 2 RTPFTEEDDAALLDYVKENERQGGSVSGNKIWKELEEKH-----PTRHTWQSWRDRYLKHLRG 59 (65)
T ss_dssp -----HHHHHHHHHHHHHT--STTTTTSSHHHHHHHHS------SSS--SHHHHHHHHHHT--
T ss_pred CCCCCHHHHHHHHHHHHHhccCCCCCchHHHHHHHHHHc-----CCCCCHHHHHHHHHHHHhc
Confidence 678999999999999976532 2 366666531 2489999999999765544
No 40
>KOG0051 consensus RNA polymerase I termination factor, Myb superfamily [Transcription]
Probab=86.46 E-value=0.61 Score=48.34 Aligned_cols=53 Identities=28% Similarity=0.480 Sum_probs=44.3
Q ss_pred CCCCCCCHHHHHHHHHHHH-------hh------------------CCCCccccccccccCccCCCCCHHhHHHHHHhhc
Q 024081 3 NPKQKWTAEEEEALRAGVA-------KH------------------GTGKWKNIQRDPEFNPFLFSRSNIDLKDKWRNMS 57 (272)
Q Consensus 3 ~~r~~WT~EEe~~L~~GV~-------Ky------------------G~GkW~~I~~~~~f~~~l~~RT~vdLKDKWRnl~ 57 (272)
+.+..||-||++.|+..|+ .| -..+|..|..+ +..|+.++|+-||-.|.
T Consensus 434 ~~r~~Ws~eEe~~Llk~V~~~~~~~~q~q~~n~~~~~q~sp~s~~~d~I~Wt~vse~------~~TR~~~qCr~Kw~kl~ 507 (607)
T KOG0051|consen 434 RNRGAWSIEEEEKLLKTVNEMIREALQPQASNTDTGLQESPESTLKDDINWTLVSEM------LGTRSRIQCRYKWYKLT 507 (607)
T ss_pred cccCcchHHHHHHHHHHHHHHHHHhhcccccccchhhhcCccccccCCcchhhhhHh------hcCCCcchHHHHHHHHH
Confidence 4789999999999999996 33 23489999884 67999999999999998
Q ss_pred cCch
Q 024081 58 VSAP 61 (272)
Q Consensus 58 ~~~~ 61 (272)
...+
T Consensus 508 ~~~s 511 (607)
T KOG0051|consen 508 TSPS 511 (607)
T ss_pred hhHH
Confidence 8764
No 41
>KOG2656 consensus DNA methyltransferase 1-associated protein-1 [Chromatin structure and dynamics; Transcription]
Probab=85.28 E-value=0.88 Score=45.06 Aligned_cols=51 Identities=20% Similarity=0.310 Sum_probs=40.9
Q ss_pred CCCCHHHHHHHHHHHHhhCCCCccccccccccCccCCCCCHHhHHHHHHhhc
Q 024081 6 QKWTAEEEEALRAGVAKHGTGKWKNIQRDPEFNPFLFSRSNIDLKDKWRNMS 57 (272)
Q Consensus 6 ~~WT~EEe~~L~~GV~KyG~GkW~~I~~~~~f~~~l~~RT~vdLKDKWRnl~ 57 (272)
.-||.+|.+.|.+..++|.- .|--|..-|.-..|-.+||--||||||-..+
T Consensus 131 n~WskeETD~LF~lck~fDL-Rf~VIaDRyd~qq~~~sRTvEdLKeRyY~v~ 181 (445)
T KOG2656|consen 131 NSWSKEETDYLFDLCKRFDL-RFFVIADRYDNQQYKKSRTVEDLKERYYSVC 181 (445)
T ss_pred ccccHHHHHHHHHHHHhcCe-eEEEEeeccchhhccccccHHHHHHHHHHHH
Confidence 45999999999999999999 9999998652222335799999999984433
No 42
>PF12776 Myb_DNA-bind_3: Myb/SANT-like DNA-binding domain; InterPro: IPR024752 This domain, found in a range of uncharacterised proteins, may be related to Myb/SANT-like DNA binding domains.
Probab=79.35 E-value=1.6 Score=33.36 Aligned_cols=52 Identities=29% Similarity=0.596 Sum_probs=37.3
Q ss_pred CCCHHHHHHHHHHHHhh---CC----C-----CccccccccccCccC-CCCCHHhHHHHHHhhccCc
Q 024081 7 KWTAEEEEALRAGVAKH---GT----G-----KWKNIQRDPEFNPFL-FSRSNIDLKDKWRNMSVSA 60 (272)
Q Consensus 7 ~WT~EEe~~L~~GV~Ky---G~----G-----kW~~I~~~~~f~~~l-~~RT~vdLKDKWRnl~~~~ 60 (272)
.||++++..|++.+... |. | .|..|... |...+ ..-|..+|++||..|.+.=
T Consensus 1 ~Wt~~~~~~ll~~~~e~~~~g~~~~~~~fk~~~w~~i~~~--~~~~~~~~~t~~qlknk~~~lk~~y 65 (96)
T PF12776_consen 1 SWTPEMTRFLLDLLIEQINKGNRPTNGGFKKEGWNNIAEE--FNEKTGLNYTKKQLKNKWKTLKKDY 65 (96)
T ss_pred CCChHHHHHHHHHHHHHHHhCCCCCCCCcCHHHHHHHHHH--HHHHhCCcccHHHHHHHHHHHHHHH
Confidence 59999999999998654 22 2 36667763 44322 4567899999998887754
No 43
>PF09420 Nop16: Ribosome biogenesis protein Nop16; InterPro: IPR019002 Nucleolar protein 16 (Nop16) is a protein involved in the biogenesis of the 60S ribosomal subunit.
Probab=76.76 E-value=5.4 Score=34.43 Aligned_cols=51 Identities=24% Similarity=0.373 Sum_probs=43.5
Q ss_pred CCCCCCHHHHHHHHHHHHhhCCCCccccccccccCccCCCCCHHhHHHHHHhhc
Q 024081 4 PKQKWTAEEEEALRAGVAKHGTGKWKNIQRDPEFNPFLFSRSNIDLKDKWRNMS 57 (272)
Q Consensus 4 ~r~~WT~EEe~~L~~GV~KyG~GkW~~I~~~~~f~~~l~~RT~vdLKDKWRnl~ 57 (272)
+...-|..|...+...|+|||. .+..+..|..++. -..|..||+.+.+.+.
T Consensus 113 ~~~~ls~~e~~~i~~Li~KhGd-Dy~aMarD~KLN~--~Q~T~~qlrrki~~~k 163 (164)
T PF09420_consen 113 KPRRLSEREIEYIEYLIEKHGD-DYKAMARDRKLNY--MQHTPGQLRRKIRKYK 163 (164)
T ss_pred CCCCCCHHHHHHHHHHHHHHCc-cHHHHhccCCCCc--ccCCHHHHHHHHHHhc
Confidence 5677899999999999999997 9999999987663 4689999999877653
No 44
>KOG0050 consensus mRNA splicing protein CDC5 (Myb superfamily) [RNA processing and modification; Cell cycle control, cell division, chromosome partitioning]
Probab=75.41 E-value=2.2 Score=43.82 Aligned_cols=48 Identities=23% Similarity=0.458 Sum_probs=41.9
Q ss_pred CCCCCHHHHHHHHHHHHhhCCCCccccccccccCccCCCCCHHhHHHHHHhhccCc
Q 024081 5 KQKWTAEEEEALRAGVAKHGTGKWKNIQRDPEFNPFLFSRSNIDLKDKWRNMSVSA 60 (272)
Q Consensus 5 r~~WT~EEe~~L~~GV~KyG~GkW~~I~~~~~f~~~l~~RT~vdLKDKWRnl~~~~ 60 (272)
+--|+.|||+.|+....-+-. .|..|.. +-+||..+|-.||-+++-..
T Consensus 59 ~tews~eederlLhlakl~p~-qwrtIa~-------i~gr~~~qc~eRy~~ll~~~ 106 (617)
T KOG0050|consen 59 KTEWSREEDERLLHLAKLEPT-QWRTIAD-------IMGRTSQQCLERYNNLLDVY 106 (617)
T ss_pred hhhhhhhHHHHHHHHHHhcCC-ccchHHH-------HhhhhHHHHHHHHHHHHHHH
Confidence 457999999999999888877 9999997 46999999999998887644
No 45
>PF08672 APC2: Anaphase promoting complex (APC) subunit 2; InterPro: IPR014786 The anaphase-promoting complex (APC) or cyclosome is a multi-subunit E3 protein ubiquitin ligase that regulates important events in mitosis such as the initiation of anaphase and exit from telophase. The APC, in conjunction with other enzymes, assembles multi-ubiquitin chains on a variety of regulatory proteins, thereby targeting them for proteolysis by the 26S proteasome. Anaphase is initiated when the APC triggers the destruction of securin, thereby allowing the protease, separase, to disrupt sister-chromatid cohesion. Securin ubiquitination by the APC is inhibited by cyclin-dependent kinase 1 (Cdk1)-dependent phosphorylation []. Forkhead Box M1 (FoxM1), which is a transcription factor that is over-expressed in many cancers, is degraded in late mitosis and early G1 phase by the APC/cyclosome (APC/C) E3 ubiquitin ligase []. The APC/C targets mitotic cyclins for destruction in mitosis and G1 phase and is then inactivated at S phase. It thereby generates alternating states of high and low cyclin-Cdk activity, which is required for the alternation of mitosis and DNA replication []. The APC/C is composed of at least 13 subunits that stay tightly associated throughout the cell cycle: APC1, APC2, APC4, APC5, APC9, APC11, CDC16, CDC23, CDC26, CDC27, DOC1, MND2 and SWM1[], []. In fission yeast the 13 subunits are known as: Apc1, Apc2, Nuc2, Apc4, Apc5, Cut9, Apc8, Apc10, Apc11, Hcn1, Apc13, Apc14 and Apc15 []. This entry represents a C-terminal domain found in APC subunit 2. ; PDB: 1LDD_A.
Probab=70.62 E-value=3.8 Score=30.14 Aligned_cols=26 Identities=35% Similarity=0.385 Sum_probs=21.8
Q ss_pred HHHHHHHHHhhhccCceeeecccccc
Q 024081 151 RRLLSSRLRRLVAQEKLEKVQNCFKV 176 (272)
Q Consensus 151 ~~~L~~~LKrlV~~GkLvkvK~sykl 176 (272)
...|..-|-++|+.|+|+.+.|+|||
T Consensus 35 ~~eL~~fL~~lv~e~~L~~~~G~YkL 60 (60)
T PF08672_consen 35 LEELQEFLDRLVEEGKLECSGGSYKL 60 (60)
T ss_dssp HHHHHHHHHHHHHTTSEE--TTEEEE
T ss_pred HHHHHHHHHHHHHCCcEEecCCEEeC
Confidence 36799999999999999999999996
No 46
>PF11839 DUF3359: Protein of unknown function (DUF3359); InterPro: IPR021793 This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are about 80 amino acids in length.
Probab=69.39 E-value=34 Score=27.68 Aligned_cols=50 Identities=28% Similarity=0.235 Sum_probs=32.6
Q ss_pred CcHHHHHHHHHHHhHHhhhhhhhHHHHHHHHHHHHHhHHhHHHHHHHHHH
Q 024081 209 DTVQEAAAAAAGQVADAENKSFVAAEAVKEAERVSRMAEDTDSLLQLAKE 258 (272)
Q Consensus 209 ~t~~eAa~aAA~~VAEAE~~~~~A~eA~~eae~~~~~ae~a~~~~~la~e 258 (272)
.|++++-..+.-+-..|+.+...|.+|...|+.+.+.|+.++.-++=|.|
T Consensus 35 ~~a~~a~~~a~~a~~~A~~A~~~AdeA~~kA~~A~aaA~~Aqq~A~eAne 84 (96)
T PF11839_consen 35 STAEQAQATAASAQSAAASAQQRADEAASKADAALAAAEAAQQTADEANE 84 (96)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34555555555555566666667777777777777777777766665554
No 47
>PF04504 DUF573: Protein of unknown function, DUF573; InterPro: IPR007592 This is a family of uncharacterised proteins.
Probab=65.46 E-value=5.5 Score=31.81 Aligned_cols=57 Identities=21% Similarity=0.331 Sum_probs=37.8
Q ss_pred CCCCCCHHHHHHHHHHHHhh----CCCCcccccccccc-Cc-cCCCCCHHhHHHHHHhhccCc
Q 024081 4 PKQKWTAEEEEALRAGVAKH----GTGKWKNIQRDPEF-NP-FLFSRSNIDLKDKWRNMSVSA 60 (272)
Q Consensus 4 ~r~~WT~EEe~~L~~GV~Ky----G~GkW~~I~~~~~f-~~-~l~~RT~vdLKDKWRnl~~~~ 60 (272)
..+.||+++|=.|++|+--| |.+....+..-++| .. +-..=|..||.||-|.|.+.-
T Consensus 3 ~qR~WS~eDEi~iL~gl~~~~~~~G~~p~~d~~~f~~~vk~~l~~~~s~~Ql~~KirrLK~Ky 65 (98)
T PF04504_consen 3 FQRLWSEEDEIVILQGLIDFRAKTGKSPQPDMNAFYDFVKGSLSFDVSKNQLYDKIRRLKKKY 65 (98)
T ss_pred CcCCCCchHHHHHHHHHHHHHHhcCCCCCccHHHHHHHHHHHccCCCCHHHHHHHHHHHHHHH
Confidence 46789999999999999888 75444332211111 00 112347899999999997764
No 48
>PF14947 HTH_45: Winged helix-turn-helix; PDB: 1XSX_B 1R7J_A.
Probab=62.31 E-value=7 Score=29.46 Aligned_cols=56 Identities=18% Similarity=0.327 Sum_probs=38.2
Q ss_pred HHHHHHHHHhcCCCCCCCHHHHHHHHHhhcCCCccHHHHHHHHHHhhhccCceeeeccccccCC
Q 024081 115 NALIFEAISALKEPNGSDVSAILSYIEQRLEVPPNFRRLLSSRLRRLVAQEKLEKVQNCFKVKE 178 (272)
Q Consensus 115 ~~MI~EAI~~Lker~GSS~~AI~kyIe~~y~v~~nf~~~L~~~LKrlV~~GkLvkvK~sykl~~ 178 (272)
.++|++=+..+. .+|.+.+-|.... +++ -..+...|+.|+..|-+...++.|+|.+
T Consensus 5 ~~Ii~~IL~~l~-~~~~~~t~i~~~~----~L~---~~~~~~yL~~L~~~gLI~~~~~~Y~lTe 60 (77)
T PF14947_consen 5 LEIIFDILKILS-KGGAKKTEIMYKA----NLN---YSTLKKYLKELEEKGLIKKKDGKYRLTE 60 (77)
T ss_dssp THHHHHHHHHH--TT-B-HHHHHTTS----T-----HHHHHHHHHHHHHTTSEEEETTEEEE-H
T ss_pred HHHHHHHHHHHH-cCCCCHHHHHHHh----CcC---HHHHHHHHHHHHHCcCeeCCCCEEEECc
Confidence 467778788877 6777777766222 221 2568889999999999988888999965
No 49
>COG5118 BDP1 Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=60.67 E-value=10 Score=37.82 Aligned_cols=50 Identities=18% Similarity=0.305 Sum_probs=44.2
Q ss_pred CCCCCCHHHHHHHHHHHHhhCCCCccccccccccCccCCCCCHHhHHHHHHhhccCc
Q 024081 4 PKQKWTAEEEEALRAGVAKHGTGKWKNIQRDPEFNPFLFSRSNIDLKDKWRNMSVSA 60 (272)
Q Consensus 4 ~r~~WT~EEe~~L~~GV~KyG~GkW~~I~~~~~f~~~l~~RT~vdLKDKWRnl~~~~ 60 (272)
.--+||.+|-+.+..++..+|. .+..|.. .|+.|...|+|-||.+--+.+
T Consensus 364 ~~~~Ws~~e~ekFYKALs~wGt-dF~LIs~------lfP~R~RkqIKaKfi~Eek~n 413 (507)
T COG5118 364 GALRWSKKEIEKFYKALSIWGT-DFSLISS------LFPNRERKQIKAKFIKEEKVN 413 (507)
T ss_pred CCCcccHHHHHHHHHHHHHhcc-hHHHHHH------hcCchhHHHHHHHHHHHhhhC
Confidence 3458999999999999999999 8999998 468999999999998877765
No 50
>PRK13923 putative spore coat protein regulator protein YlbO; Provisional
Probab=60.18 E-value=3 Score=36.95 Aligned_cols=58 Identities=17% Similarity=0.197 Sum_probs=37.7
Q ss_pred CCCCCCCCCHHHHHHHHHHHHhhCCCCccccccccccCccCCCCCHHhHHHHHHhhccC
Q 024081 1 MGNPKQKWTAEEEEALRAGVAKHGTGKWKNIQRDPEFNPFLFSRSNIDLKDKWRNMSVS 59 (272)
Q Consensus 1 mg~~r~~WT~EEe~~L~~GV~KyG~GkW~~I~~~~~f~~~l~~RT~vdLKDKWRnl~~~ 59 (272)
|--....||.|+|..|-.-|-+|+.--=.++.- ++.-...-+||...|.+||-..++.
T Consensus 1 mk~rqdawt~e~d~llae~vl~~i~eg~tql~a-fe~~g~~L~rt~aac~fRwNs~vrk 58 (170)
T PRK13923 1 MKTRQDAWTQERDGLLAEVVLRHIREGGTQLKA-FEEVGDALKRTAAACGFRWNSVVRK 58 (170)
T ss_pred CcchhhhhhhHHHHHHHHHHHHHHhccchHHHH-HHHHHHHHhhhHHHHHhHHHHHHHH
Confidence 445567899999999999999886511112211 1111123589999999999555553
No 51
>PF05928 Zea_mays_MuDR: Zea mays MURB-like protein (MuDR); InterPro: IPR009227 This family consists of several Zea mays (Maize) specific MURB-like proteins. The transposition of Mu elements underlying Mutator activity in maize requires a transcriptionally active MuDR element. Despite variation in MuDR copy number and RNA levels in Mutator lines, transposition events are consistently late in plant development, and Mu excision frequencies are similar [].
Probab=60.12 E-value=21 Score=31.88 Aligned_cols=27 Identities=37% Similarity=0.390 Sum_probs=20.8
Q ss_pred HHHHHHHHHHHhHHhhhhhhhHHHHHH
Q 024081 211 VQEAAAAAAGQVADAENKSFVAAEAVK 237 (272)
Q Consensus 211 ~~eAa~aAA~~VAEAE~~~~~A~eA~~ 237 (272)
+.|||.+||-+-+||....+.||--+|
T Consensus 12 ~v~aaraaavaa~earc~~~vaekea~ 38 (207)
T PF05928_consen 12 VVDAARAAAVAASEARCVVFVAEKEAR 38 (207)
T ss_pred HHHHHHHHHHHHhhhhhhhhhhhHHHH
Confidence 468889999888888888887764433
No 52
>PF05402 PqqD: Coenzyme PQQ synthesis protein D (PqqD); InterPro: IPR008792 This family contains several bacterial coenzyme PQQ synthesis protein D (PqqD) sequences. This protein is required for coenzyme pyrrolo-quinoline-quinone (PQQ) biosynthesis.; PDB: 3G2B_A.
Probab=58.02 E-value=19 Score=25.74 Aligned_cols=39 Identities=15% Similarity=0.240 Sum_probs=29.3
Q ss_pred CCCCHHHHHHHHHhhcCCCcc-HHHHHHHHHHhhhccCce
Q 024081 129 NGSDVSAILSYIEQRLEVPPN-FRRLLSSRLRRLVAQEKL 167 (272)
Q Consensus 129 ~GSS~~AI~kyIe~~y~v~~n-f~~~L~~~LKrlV~~GkL 167 (272)
++.|...|.+.+.++|++++. ...-+..-|..|...|-|
T Consensus 28 g~~t~~ei~~~l~~~y~~~~~~~~~dv~~fl~~L~~~glI 67 (68)
T PF05402_consen 28 GPRTVEEIVDALAEEYDVDPEEAEEDVEEFLEQLREKGLI 67 (68)
T ss_dssp SSS-HHHHHHHHHHHTT--HHHHHHHHHHHHHHHHHTT--
T ss_pred CCCCHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHCcCc
Confidence 469999999999999988654 677788888999888865
No 53
>PF11626 Rap1_C: TRF2-interacting telomeric protein/Rap1 - C terminal domain; InterPro: IPR021661 This family of proteins represents the C-terminal domain of the protein Rap-1, which plays a distinct role in silencing at the silent mating-type loci and telomeres []. The Rap-1 C terminus adopts an all-helical fold. Rap1 carries out its function by recruiting the Sir3 and Sir4 proteins to chromatin via its C-terminal domain []. ; PDB: 3K6G_C 3CZ6_A 3OWT_A.
Probab=46.47 E-value=19 Score=27.86 Aligned_cols=21 Identities=38% Similarity=0.683 Sum_probs=12.0
Q ss_pred CCCCCHHHHHHH--------HHHHHhhCC
Q 024081 5 KQKWTAEEEEAL--------RAGVAKHGT 25 (272)
Q Consensus 5 r~~WT~EEe~~L--------~~GV~KyG~ 25 (272)
.+-||+|+|+.| ...++|||.
T Consensus 47 ~GiWT~eDD~~L~~~~~~~~~~L~~khG~ 75 (87)
T PF11626_consen 47 PGIWTPEDDEMLRSGDKDDIERLIKKHGE 75 (87)
T ss_dssp TT---HHHHHHHTS--HHHHHHHHHHH-H
T ss_pred CCCcCHHHHHHHHcCCHHHHHHHHHHhCH
Confidence 567999999999 334456664
No 54
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=45.94 E-value=87 Score=22.94 Aligned_cols=59 Identities=15% Similarity=0.195 Sum_probs=41.6
Q ss_pred CCCHHHHHHHHHHhcCCCCCCCHHHHHHHHHhhcCCCccHHHHHHHHHHhhhccCceeeec---cccccC
Q 024081 111 APKYNALIFEAISALKEPNGSDVSAILSYIEQRLEVPPNFRRLLSSRLRRLVAQEKLEKVQ---NCFKVK 177 (272)
Q Consensus 111 hp~y~~MI~EAI~~Lker~GSS~~AI~kyIe~~y~v~~nf~~~L~~~LKrlV~~GkLvkvK---~sykl~ 177 (272)
+..+.+-|++.|..-.++ |.+..-|++-+ +++ +.-++.+|.+|...|.+++.. +.|+|.
T Consensus 4 ~~~~~~~IL~~L~~~g~~-~~ta~eLa~~l----gl~---~~~v~r~L~~L~~~G~V~~~~~~~~~W~i~ 65 (68)
T smart00550 4 QDSLEEKILEFLENSGDE-TSTALQLAKNL----GLP---KKEVNRVLYSLEKKGKVCKQGGTPPLWKLT 65 (68)
T ss_pred chHHHHHHHHHHHHCCCC-CcCHHHHHHHH----CCC---HHHHHHHHHHHHHCCCEEecCCCCCceEee
Confidence 345677788888765333 58877776655 444 357899999999999999853 566664
No 55
>PF05732 RepL: Firmicute plasmid replication protein (RepL); InterPro: IPR008813 This entry consists of proteins thought to be involved in plasmid replication. ; GO: 0006260 DNA replication, 0006276 plasmid maintenance
Probab=43.14 E-value=67 Score=27.93 Aligned_cols=63 Identities=16% Similarity=0.349 Sum_probs=45.8
Q ss_pred HHHHHHHHHHhcCCCCCCCHHHHHHHHHhhcC----CCccH----------HHHHHHHHHhhhccCceeeec-cccccCC
Q 024081 114 YNALIFEAISALKEPNGSDVSAILSYIEQRLE----VPPNF----------RRLLSSRLRRLVAQEKLEKVQ-NCFKVKE 178 (272)
Q Consensus 114 y~~MI~EAI~~Lker~GSS~~AI~kyIe~~y~----v~~nf----------~~~L~~~LKrlV~~GkLvkvK-~sykl~~ 178 (272)
|.+.|...+.- -|.....|..||-++.+ +-... ..-++..|+.|.+.|-|.+++ |.|.|.|
T Consensus 42 ~~~ni~~~l~l----~g~k~~~Vl~~il~~~d~~N~v~~t~~~ia~~l~iS~~Tv~r~ik~L~e~~iI~k~~~G~Y~iNP 117 (165)
T PF05732_consen 42 YLENIIKVLDL----IGNKAFRVLMYILENMDKDNAVVATQKEIAEKLGISKPTVSRAIKELEEKNIIKKIRNGAYMINP 117 (165)
T ss_pred HHHHHHHHhhh----hchhHHHHHHHHHHhcCCCCeEEeeHHHHHHHhCCCHHHHHHHHHHHHhCCcEEEccCCeEEECc
Confidence 44555554443 46678999999998752 10011 356899999999999999988 7999999
Q ss_pred cc
Q 024081 179 DA 180 (272)
Q Consensus 179 ~~ 180 (272)
..
T Consensus 118 ~~ 119 (165)
T PF05732_consen 118 NF 119 (165)
T ss_pred HH
Confidence 76
No 56
>PF08784 RPA_C: Replication protein A C terminal; InterPro: IPR014892 This protein corresponds to the C-terminal of the single stranded DNA binding protein RPA (replication protein A). RPA is involved in many DNA metabolic pathways including DNA replication, DNA repair, recombination, cell cycle and DNA damage checkpoints. ; PDB: 1QUQ_C 2PQA_C 3KDF_B 2Z6K_B 2PI2_B 1L1O_E 1DPU_A 1Z1D_A.
Probab=41.34 E-value=57 Score=25.39 Aligned_cols=53 Identities=11% Similarity=0.147 Sum_probs=40.5
Q ss_pred CCCCHHHHHHHHHHh-cCCCCCCCHHHHHHHHHhhcCCCccHHHHHHHHHHhhhccCceee
Q 024081 110 SAPKYNALIFEAISA-LKEPNGSDVSAILSYIEQRLEVPPNFRRLLSSRLRRLVAQEKLEK 169 (272)
Q Consensus 110 shp~y~~MI~EAI~~-Lker~GSS~~AI~kyIe~~y~v~~nf~~~L~~~LKrlV~~GkLvk 169 (272)
...+..++|++.|.. .....|.++.-|.+-+ .++ ..-|+.+|..|+..|.|.-
T Consensus 44 ~~~~~~~~Vl~~i~~~~~~~~Gv~v~~I~~~l----~~~---~~~v~~al~~L~~eG~IYs 97 (102)
T PF08784_consen 44 GLSPLQDKVLNFIKQQPNSEEGVHVDEIAQQL----GMS---ENEVRKALDFLSNEGHIYS 97 (102)
T ss_dssp -S-HHHHHHHHHHHC----TTTEEHHHHHHHS----TS----HHHHHHHHHHHHHTTSEEE
T ss_pred CCCHHHHHHHHHHHhcCCCCCcccHHHHHHHh----CcC---HHHHHHHHHHHHhCCeEec
Confidence 355679999999999 7778999999999877 333 4589999999999999864
No 57
>PF13325 MCRS_N: N-terminal region of micro-spherule protein
Probab=40.72 E-value=42 Score=30.46 Aligned_cols=49 Identities=12% Similarity=0.394 Sum_probs=36.5
Q ss_pred CCCHHHHHHHHHHHHhhCCCCccccccccccCccCCCCCHHhHHHHHHhhccCc
Q 024081 7 KWTAEEEEALRAGVAKHGTGKWKNIQRDPEFNPFLFSRSNIDLKDKWRNMSVSA 60 (272)
Q Consensus 7 ~WT~EEe~~L~~GV~KyG~GkW~~I~~~~~f~~~l~~RT~vdLKDKWRnl~~~~ 60 (272)
+|+++.|-.|+.+|..-. .=..|...-.|+ ..-|-..+.+||..|+-..
T Consensus 1 rW~~~DDl~Li~av~~~~--~L~~v~~gvkFS---~~fT~~Ei~~RW~~llyd~ 49 (199)
T PF13325_consen 1 RWKPEDDLLLINAVEQTN--DLESVHLGVKFS---CKFTLQEIEERWYALLYDP 49 (199)
T ss_pred CCCchhhHHHHHHHHHhc--CHHHHHccCCcC---CcCcHHHHHHHHHHHHcCh
Confidence 699999999999999642 333444332444 5678899999999988765
No 58
>PF05066 HARE-HTH: HB1, ASXL, restriction endonuclease HTH domain; InterPro: IPR007759 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. The delta protein is a dispensable subunit of Bacillus subtilis RNA polymerase (RNAP) that has major effects on the biochemical properties of the purified enzyme. In the presence of delta, RNAP displays an increased specificity of transcription, a decreased affinity for nucleic acids, and an increased efficiency of RNA synthesis because of enhanced recycling []. The delta protein, contains two distinct regions, an N-terminal domain and a glutamate and aspartate residue-rich C-terminal region [].; GO: 0003677 DNA binding, 0006351 transcription, DNA-dependent; PDB: 2KRC_A.
Probab=39.83 E-value=77 Score=23.14 Aligned_cols=62 Identities=11% Similarity=0.135 Sum_probs=35.4
Q ss_pred CHHHHHHHHHHhcCCCCCCCHHHHHHHHHhhcCCC---ccHHHHHHHHHHhh--hccCceeee-cccccc
Q 024081 113 KYNALIFEAISALKEPNGSDVSAILSYIEQRLEVP---PNFRRLLSSRLRRL--VAQEKLEKV-QNCFKV 176 (272)
Q Consensus 113 ~y~~MI~EAI~~Lker~GSS~~AI~kyIe~~y~v~---~nf~~~L~~~LKrl--V~~GkLvkv-K~sykl 176 (272)
+|.+.+.+.+...+ ...+..-|.+.|.+..... .+....|+..|-.- -..|.|+++ .|.|-|
T Consensus 2 t~~eaa~~vL~~~~--~pm~~~eI~~~i~~~~~~~~~~k~p~~~i~a~ly~~~~~~d~~F~~vg~~~~~L 69 (72)
T PF05066_consen 2 TFKEAAYEVLEEAG--RPMTFKEIWEEIQERGLYKKSGKTPEATIAAQLYTDIKNEDSRFVKVGPGRWGL 69 (72)
T ss_dssp -HHHHHHHHHHHH---S-EEHHHHHHHHHHHHTS---GGGGGHHHH-HHHHHHH-T-SS-EESSSSEEE-
T ss_pred CHHHHHHHHHHhcC--CCcCHHHHHHHHHHhCCCCcccCCHHHHHHHHHHHHcccCCCCEEEeCCCcEEe
Confidence 35666666666666 5689999999999876332 23334444444332 478889998 577765
No 59
>COG4742 Predicted transcriptional regulator [Transcription]
Probab=38.64 E-value=42 Score=31.66 Aligned_cols=48 Identities=10% Similarity=0.192 Sum_probs=34.9
Q ss_pred HhcCCCCCCCHHHHHHHHHhhcCCCccHHHHHHHHHHhhhccCceeeeccccccCC
Q 024081 123 SALKEPNGSDVSAILSYIEQRLEVPPNFRRLLSSRLRRLVAQEKLEKVQNCFKVKE 178 (272)
Q Consensus 123 ~~Lker~GSS~~AI~kyIe~~y~v~~nf~~~L~~~LKrlV~~GkLvkvK~sykl~~ 178 (272)
.-|++ +.-+..-|+.++.-. ...+..+||+|...|-++|..+.|+|++
T Consensus 20 llL~e-gPkti~EI~~~l~vs-------~~ai~pqiKkL~~~~LV~~~~~~Y~LS~ 67 (260)
T COG4742 20 LLLKE-GPKTIEEIKNELNVS-------SSAILPQIKKLKDKGLVVQEGDRYSLSS 67 (260)
T ss_pred HHHHh-CCCCHHHHHHHhCCC-------cHHHHHHHHHHhhCCCEEecCCEEEecc
Confidence 34444 334566666655422 3578889999999999999999999975
No 60
>cd00092 HTH_CRP helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family.
Probab=37.34 E-value=39 Score=23.49 Aligned_cols=41 Identities=17% Similarity=0.313 Sum_probs=29.4
Q ss_pred CCHHHHHHHHHhhcCCCccHHHHHHHHHHhhhccCceeeec-cccccCC
Q 024081 131 SDVSAILSYIEQRLEVPPNFRRLLSSRLRRLVAQEKLEKVQ-NCFKVKE 178 (272)
Q Consensus 131 SS~~AI~kyIe~~y~v~~nf~~~L~~~LKrlV~~GkLvkvK-~sykl~~ 178 (272)
.+...|+..+. ++ ...++..|+.|...|.|.... |.|.|.+
T Consensus 26 ~s~~ela~~~g----~s---~~tv~r~l~~L~~~g~i~~~~~~~~~l~~ 67 (67)
T cd00092 26 LTRQEIADYLG----LT---RETVSRTLKELEEEGLISRRGRGKYRVNP 67 (67)
T ss_pred cCHHHHHHHHC----CC---HHHHHHHHHHHHHCCCEEecCCCeEEeCC
Confidence 45555555443 22 467888999999999999887 8888753
No 61
>PF06969 HemN_C: HemN C-terminal domain; InterPro: IPR010723 Proteins containing this domain are all oxygen-independent coproporphyrinogen-III oxidases (HemN). This enzyme catalyses the oxygen-independent conversion of coproporphyrinogen-III to protoporphyrinogen-IX [], one of the last steps in haem biosynthesis. The function of this domain is unclear, but comparison to other proteins containing a radical SAM domain suggest it may be a substrate binding domain.; GO: 0004109 coproporphyrinogen oxidase activity, 0006779 porphyrin-containing compound biosynthetic process, 0055114 oxidation-reduction process, 0005737 cytoplasm; PDB: 1OLT_A.
Probab=36.43 E-value=60 Score=23.00 Aligned_cols=48 Identities=25% Similarity=0.318 Sum_probs=32.2
Q ss_pred cCCCCCCCHHHHHHHHHhhcCCCccHHHHHHHHHHhhhccCceeeeccccccCC
Q 024081 125 LKEPNGSDVSAILSYIEQRLEVPPNFRRLLSSRLRRLVAQEKLEKVQNCFKVKE 178 (272)
Q Consensus 125 Lker~GSS~~AI~kyIe~~y~v~~nf~~~L~~~LKrlV~~GkLvkvK~sykl~~ 178 (272)
|.=..|.|...+. .+|. .+|...+...|..+++.|-|+...+++++++
T Consensus 15 LR~~~Gi~~~~~~----~~~g--~~~~~~~~~~l~~l~~~Gll~~~~~~l~lT~ 62 (66)
T PF06969_consen 15 LRCNEGIDLSEFE----QRFG--IDFAEEFQKELEELQEDGLLEIDGGRLRLTE 62 (66)
T ss_dssp HHHHSEEEHHHHH----HHTT----THHH-HHHHHHHHHTTSEEE-SSEEEE-T
T ss_pred HHhHCCcCHHHHH----HHHC--cCHHHHHHHHHHHHHHCCCEEEeCCEEEECc
Confidence 3335566666554 3443 2367777888999999999999999999975
No 62
>PF11839 DUF3359: Protein of unknown function (DUF3359); InterPro: IPR021793 This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are about 80 amino acids in length.
Probab=33.17 E-value=2.5e+02 Score=22.73 Aligned_cols=35 Identities=26% Similarity=0.282 Sum_probs=17.4
Q ss_pred HHHHHHHhHHhhhhhhhHHHHHHHHHHHHHhHHhH
Q 024081 215 AAAAAGQVADAENKSFVAAEAVKEAERVSRMAEDT 249 (272)
Q Consensus 215 a~aAA~~VAEAE~~~~~A~eA~~eae~~~~~ae~a 249 (272)
-.+|..+-..|+.+...|.+|.-.|+++.+.|+++
T Consensus 48 ~~~A~~A~~~AdeA~~kA~~A~aaA~~Aqq~A~eA 82 (96)
T PF11839_consen 48 QSAAASAQQRADEAASKADAALAAAEAAQQTADEA 82 (96)
T ss_pred HHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 33344444444444445555555555555555544
No 63
>PF08220 HTH_DeoR: DeoR-like helix-turn-helix domain; InterPro: IPR001034 The deoR-type HTH domain is a DNA-binding, helix-turn-helix (HTH) domain of about 50-60 amino acids present in transcription regulators of the deoR family, involved in sugar catabolism. This family of prokaryotic regulators is named after the Escherichia coli protein DeoR, a repressor of the deo operon, which encodes nucleotide and deoxyribonucleotide catabolic enzymes. DeoR also negatively regulates the expression of nupG and tsx, a nucleoside-specific transport protein and a channel-forming protein, respectively. DeoR-like transcription repressors occur in diverse bacteria as regulators of sugar and nucleoside metabolic systems. The effector molecules for deoR-like regulators are generally phosphorylated intermediates of the relevant metabolic pathway. The DNA-binding deoR-type HTH domain occurs usually in the N-terminal part. The C-terminal part can contain an effector-binding domain and/or an oligomerisation domain. DeoR occurs as an octamer, whilst glpR and agaR are tetramers. Several operators may be bound simultaneously, which could facilitate DNA looping [, ].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular
Probab=32.39 E-value=52 Score=23.29 Aligned_cols=27 Identities=11% Similarity=0.190 Sum_probs=22.9
Q ss_pred HHHHHHHHhhhccCceeeeccccccCC
Q 024081 152 RLLSSRLRRLVAQEKLEKVQNCFKVKE 178 (272)
Q Consensus 152 ~~L~~~LKrlV~~GkLvkvK~sykl~~ 178 (272)
.-++.-|..|...|.|.++.|.+.+..
T Consensus 29 ~TiRRDl~~L~~~g~i~r~~GG~~~~~ 55 (57)
T PF08220_consen 29 MTIRRDLNKLEKQGLIKRTHGGAVLND 55 (57)
T ss_pred HHHHHHHHHHHHCCCEEEEcCEEEeCC
Confidence 457788899999999999999887754
No 64
>cd01392 HTH_LacI Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators. HTH-DNA binding domain of the LacI (lactose operon repressor) family of bacterial transcriptional regulators and their putative homologs found in plants. The LacI family has more than 500 members distributed among almost all bacterial species. The monomeric proteins of the LacI family contain common structural features that include a small DNA-binding domain with a helix-turn-helix motif in the N-terminus, a regulatory ligand-binding domain which exhibits the type I periplasmic binding protein fold in the C-terminus for oligomerization and for effector binding, and an approximately 18-amino acid linker connecting these two functional domains. In LacI-like transcriptional regulators, the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions. When the C-terminal domain of the LacI family repre
Probab=31.23 E-value=43 Score=22.39 Aligned_cols=36 Identities=11% Similarity=0.205 Sum_probs=25.9
Q ss_pred cCCCCCCCHHHHHHHHHhhcCCCccHHHHHHHHHHh
Q 024081 125 LKEPNGSDVSAILSYIEQRLEVPPNFRRLLSSRLRR 160 (272)
Q Consensus 125 Lker~GSS~~AI~kyIe~~y~v~~nf~~~L~~~LKr 160 (272)
|.+.-|.|.++|..++..+..+.+.....+...++.
T Consensus 3 lA~~~gvs~~tvs~~l~g~~~vs~~~~~~i~~~~~~ 38 (52)
T cd01392 3 IARAAGVSVATVSRVLNGKPRVSEETRERVLAAAEE 38 (52)
T ss_pred HHHHHCcCHHHHHHHHcCCCCCCHHHHHHHHHHHHH
Confidence 455678999999999988877766666655555544
No 65
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=30.79 E-value=1.6e+02 Score=21.69 Aligned_cols=52 Identities=12% Similarity=0.252 Sum_probs=37.1
Q ss_pred HHHHHHhcCCCCCCCHHHHHHHHHhhcCCCccHHHHHHHHHHhhhccCceeee--ccccccCC
Q 024081 118 IFEAISALKEPNGSDVSAILSYIEQRLEVPPNFRRLLSSRLRRLVAQEKLEKV--QNCFKVKE 178 (272)
Q Consensus 118 I~EAI~~Lker~GSS~~AI~kyIe~~y~v~~nf~~~L~~~LKrlV~~GkLvkv--K~sykl~~ 178 (272)
|++.|..- +.+.+...|...+ +++ +..+...|+.|+..|-|.+. .+.|.+.+
T Consensus 10 Il~~l~~~--~~~~t~~~ia~~l----~i~---~~tv~r~l~~L~~~g~l~~~~~~~~y~l~~ 63 (91)
T smart00346 10 VLRALAEE--PGGLTLAELAERL----GLS---KSTAHRLLNTLQELGYVEQDGQNGRYRLGP 63 (91)
T ss_pred HHHHHHhC--CCCcCHHHHHHHh----CCC---HHHHHHHHHHHHHCCCeeecCCCCceeecH
Confidence 45555432 2578999998887 333 46788889999999999985 35677754
No 66
>PF13463 HTH_27: Winged helix DNA-binding domain; PDB: 3GFL_A 2YR2_B 3GFM_A 3GFJ_A 3GF2_A 3GEZ_A 2GXG_A 3GFI_A 2EB7_A.
Probab=29.50 E-value=85 Score=21.90 Aligned_cols=47 Identities=13% Similarity=0.173 Sum_probs=28.9
Q ss_pred HHHHHHHHhcCCCCCCCHHHHHHHHHhhcCCCccHHHHHHHHHHhhhccCceeeec
Q 024081 116 ALIFEAISALKEPNGSDVSAILSYIEQRLEVPPNFRRLLSSRLRRLVAQEKLEKVQ 171 (272)
Q Consensus 116 ~MI~EAI~~Lker~GSS~~AI~kyIe~~y~v~~nf~~~L~~~LKrlV~~GkLvkvK 171 (272)
..|+..|. .+..+.+...|..+..-. ...++..|++|+..|-|.+..
T Consensus 6 ~~vL~~l~--~~~~~~t~~~l~~~~~~~-------~~~vs~~i~~L~~~glv~~~~ 52 (68)
T PF13463_consen 6 WQVLRALA--HSDGPMTQSDLAERLGIS-------KSTVSRIIKKLEEKGLVEKER 52 (68)
T ss_dssp HHHHHHHT----TS-BEHHHHHHHTT---------HHHHHHHHHHHHHTTSEEEEE
T ss_pred HHHHHHHH--ccCCCcCHHHHHHHHCcC-------HHHHHHHHHHHHHCCCEEecC
Confidence 34455554 245556666666554422 457889999999999998753
No 67
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=29.14 E-value=64 Score=20.79 Aligned_cols=26 Identities=19% Similarity=0.293 Sum_probs=21.2
Q ss_pred HHHHHHHHHhhhccCceeeecccccc
Q 024081 151 RRLLSSRLRRLVAQEKLEKVQNCFKV 176 (272)
Q Consensus 151 ~~~L~~~LKrlV~~GkLvkvK~sykl 176 (272)
...++..|+.|.+.|-|...++.|.|
T Consensus 22 ~~tv~~~l~~L~~~g~l~~~~~~~~i 47 (48)
T smart00419 22 RETVSRTLKRLEKEGLISREGGRIVI 47 (48)
T ss_pred HHHHHHHHHHHHHCCCEEEeCCEEEE
Confidence 35678889999999999987777765
No 68
>PF01325 Fe_dep_repress: Iron dependent repressor, N-terminal DNA binding domain; InterPro: IPR022687 The DtxR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 65 residues present in metalloregulators of the DtxR/MntR family. The family is named after Corynebacterium diphtheriae DtxR, an iron-specific diphtheria toxin repressor, and Bacillus subtilis MntR, a manganese transport regulator. Iron-responsive metalloregulators such as DtxR and IdeR occur in Gram-positive bacteria of the high GC branch, while manganese-responsive metalloregulators like MntR are described in diverse genera of Gram-positive and Gram-negative bacteria and also in Archaea [].The metalloregulators like DtxR/MntR contain the DNA-binding DtxR-type HTH domain usually in the N-terminal part. The C-terminal part contains a dimerisation domain with two metal-binding sites, although the primary metal-binding site is less conserved in the Mn(II)-regulators. Fe(II)-regulated proteins contain an SH3-like domain as a C-terminal extension, which is absent in Mn(II)-regulated MntR [, ]. Metal-ion dependent regulators orchestrate the virulence of several important human pathogens. The DtxR protein regulates the expression of diphtheria toxinin response to environmental iron concentrations. Furthermore, DtxR and IdeR control iron uptake []. Homeostasis of manganese, which is an essential nutrient, is regulated by MntR. A typical DtxR-type metalloregulator binds two divalent metal effectors per monomer, upon which allosteric changes occur that moderate binding to the cognate DNA operators. Iron-bound DtxR homodimers bind to an interrupted palindrome of 19 bp, protecting a sequence of ~30 bp. The crystal structures of iron-regulated and manganese-regulated repressors show that the DNA binding domain contains three alpha-helices and a pair of antiparallel beta-strands. Helices 2 and 3 comprise the helix-turn-helix motif and the beta-strands are called the wing []. This wHTH topology is similar to the lysR-type HTH (see PDOC00043 from PROSITEDOC). Most DtxR-type metalloregulators bind as dimers to the DNA major groove. Several proteins are known to contain a DtxR-type HTH domain. These include- Corynebacterium diphtheriae DtxR, a diphtheria toxin repressor [], which regulates the expression of the high-affinity iron uptake system, other iron-sensitive genes, and the bacteriophage tox gene. Metal-bound DtxR represses transcription by binding the tox operator; if iron is limiting, conformational changes of the wHTH disrupt DNA-binding and the diphtheria toxin is produced. Mycobacterium tuberculosis IdeR, an iron-dependent regulator that is essential for this pathogen. The regulator represses genes for iron acquisition and activates iron storage genes, and is a positive regulator of oxidative stress responses []. Bacillus subtilis MntR, a manganese transport regulator, binds Mn2+ as an effector and is a transcriptional repressor of transporters for the import of manganese. Treponema pallidum troR, a metal-dependent transcriptional repressor. Archaeoglobus fulgidus MDR1 (troR), a metal-dependent transcriptional repressor, which negatively regulates its own transcription. This entry covers the entire DtxR-type HTH domain.; GO: 0005506 iron ion binding; PDB: 3HRT_B 3HRS_A 3HRU_B 2X4H_D 1ON1_B 2HYF_C 2F5E_A 3R60_B 1ON2_B 2F5F_A ....
Probab=28.85 E-value=2.2e+02 Score=20.49 Aligned_cols=47 Identities=19% Similarity=0.201 Sum_probs=33.7
Q ss_pred HHHHHHHHHHhcCCCCCCCHHHHHHHHHhhcCCCccHHHHHHHHHHhhhccCceeee
Q 024081 114 YNALIFEAISALKEPNGSDVSAILSYIEQRLEVPPNFRRLLSSRLRRLVAQEKLEKV 170 (272)
Q Consensus 114 y~~MI~EAI~~Lker~GSS~~AI~kyIe~~y~v~~nf~~~L~~~LKrlV~~GkLvkv 170 (272)
|...|.+... +....+...|++++.-. ...++..|++|...|-+...
T Consensus 9 YL~~Iy~l~~---~~~~v~~~~iA~~L~vs-------~~tvt~ml~~L~~~GlV~~~ 55 (60)
T PF01325_consen 9 YLKAIYELSE---EGGPVRTKDIAERLGVS-------PPTVTEMLKRLAEKGLVEYE 55 (60)
T ss_dssp HHHHHHHHHH---CTSSBBHHHHHHHHTS--------HHHHHHHHHHHHHTTSEEEE
T ss_pred HHHHHHHHHc---CCCCccHHHHHHHHCCC-------hHHHHHHHHHHHHCCCEEec
Confidence 5555555443 56667888888877533 45788999999999998864
No 69
>PF01726 LexA_DNA_bind: LexA DNA binding domain; InterPro: IPR006199 This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins in bacteria. The aligned region contains a variant form of the helix-turn-helix DNA binding motif []. This domain usually at the N terminus is found associated with IPR006198 from INTERPRO the auto-proteolytic domain of LexA 3.4.21.88 from EC.; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 1LEA_A 1JHH_A 3JSP_A 1JHF_A 3JSO_B 1LEB_A 3K2Z_A.
Probab=27.95 E-value=1.4e+02 Score=22.05 Aligned_cols=22 Identities=9% Similarity=0.116 Sum_probs=18.8
Q ss_pred HHHHHHHHhhhccCceeeeccc
Q 024081 152 RLLSSRLRRLVAQEKLEKVQNC 173 (272)
Q Consensus 152 ~~L~~~LKrlV~~GkLvkvK~s 173 (272)
..+..+|+.|...|-|.+..|.
T Consensus 41 ~tv~~~L~~Le~kG~I~r~~~~ 62 (65)
T PF01726_consen 41 STVQRHLKALERKGYIRRDPGK 62 (65)
T ss_dssp HHHHHHHHHHHHTTSEEEGCCS
T ss_pred HHHHHHHHHHHHCcCccCCCCC
Confidence 4688899999999999987764
No 70
>PF08343 RNR_N: Ribonucleotide reductase N-terminal; InterPro: IPR013554 This domain is found at the N terminus of bacterial ribonucleoside-diphosphate reductases (ribonucleotide reductases, RNRs) which catalyse the formation of deoxyribonucleotides []. It occurs together with the RNR all-alpha domain (IPR013509 from INTERPRO) and the RNR barrel domain (IPR000788 from INTERPRO). ; GO: 0004748 ribonucleoside-diphosphate reductase activity, 0006260 DNA replication, 0055114 oxidation-reduction process, 0005971 ribonucleoside-diphosphate reductase complex; PDB: 1PEM_A 2BQ1_E 1PEU_A 1PEQ_A 1PEO_A.
Probab=27.82 E-value=48 Score=25.87 Aligned_cols=50 Identities=26% Similarity=0.396 Sum_probs=33.3
Q ss_pred HHHHHHhcCCCCCC-----CHHHHHHHHHhhcCCCccHH--HHHHHHHHhhhccCceee
Q 024081 118 IFEAISALKEPNGS-----DVSAILSYIEQRLEVPPNFR--RLLSSRLRRLVAQEKLEK 169 (272)
Q Consensus 118 I~EAI~~Lker~GS-----S~~AI~kyIe~~y~v~~nf~--~~L~~~LKrlV~~GkLvk 169 (272)
.+.|...+.+.+|. ++.|+..|++++- -||.. ..+..+|+-||.+|-...
T Consensus 3 ~LNn~~~~~~~~G~~~l~kD~eA~~~y~~~~V--~pnt~~F~S~~Erl~yLv~~~YYe~ 59 (82)
T PF08343_consen 3 ELNNELNIYDEDGKIQLEKDKEAVRAYFKEHV--NPNTVKFNSLKERLDYLVENDYYEK 59 (82)
T ss_dssp HHHHGGG---TTS---THHHHHHHHHHHHHTT--GGGB---SSHHHHHHHHHHTTSB-H
T ss_pred HHHHHHcCCCCCCCcCchhHHHHHHHHHHHhc--ccceeecCCHHHHHHHHHHcCcHHH
Confidence 35566677788887 7899999999864 23444 358889999999987654
No 71
>KOG3614 consensus Ca2+/Mg2+-permeable cation channels (LTRPC family) [Inorganic ion transport and metabolism; Signal transduction mechanisms]
Probab=27.67 E-value=1.2e+02 Score=34.76 Aligned_cols=34 Identities=29% Similarity=0.394 Sum_probs=26.6
Q ss_pred hHHHHHHHHHHHHHhHHhHHHHHHHHHHHHHHhc
Q 024081 231 VAAEAVKEAERVSRMAEDTDSLLQLAKEIFERCS 264 (272)
Q Consensus 231 ~A~eA~~eae~~~~~ae~a~~~~~la~ei~~~c~ 264 (272)
.|.||..+.|.++.+-+-++.|=++|.|+|++|-
T Consensus 603 lA~ea~d~~~~s~el~~~s~~f~~lAveLfd~cy 636 (1381)
T KOG3614|consen 603 LAHEAHDWHEAAKELKTLSDEFEGLAVELFDECY 636 (1381)
T ss_pred HhhhcchhhHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 3344444677777777889999999999999993
No 72
>CHL00137 rps13 ribosomal protein S13; Validated
Probab=27.20 E-value=88 Score=26.08 Aligned_cols=49 Identities=20% Similarity=0.323 Sum_probs=40.8
Q ss_pred CCCCHHHHHHHHHhhcCCCccHHHHHHHHHHhhhccCceeeeccccccC
Q 024081 129 NGSDVSAILSYIEQRLEVPPNFRRLLSSRLRRLVAQEKLEKVQNCFKVK 177 (272)
Q Consensus 129 ~GSS~~AI~kyIe~~y~v~~nf~~~L~~~LKrlV~~GkLvkvK~sykl~ 177 (272)
+-.....|.+||+++|.+..+++..++.-+++++.-|..--..+...||
T Consensus 49 t~~qi~~l~~~i~~~~~i~~dL~~~~~~dI~rl~~I~sYRG~RH~~gLP 97 (122)
T CHL00137 49 TDEQISALREIIEENYQVEGDLRRFESLNIKRLMEINCYRGRRHRLGLP 97 (122)
T ss_pred CHHHHHHHHHHHHHhCcchHHHHHHHHHHHHHHHHhCchhcccccCCCC
Confidence 3345788999999899999999999999999999998877666666665
No 73
>PF15054 DUF4535: Domain of unknown function (DUF4535)
Probab=26.60 E-value=32 Score=24.27 Aligned_cols=20 Identities=40% Similarity=0.750 Sum_probs=14.4
Q ss_pred HHHhhcCCCccHHHHHHHHHH
Q 024081 139 YIEQRLEVPPNFRRLLSSRLR 159 (272)
Q Consensus 139 yIe~~y~v~~nf~~~L~~~LK 159 (272)
||.+||+|| |.+.++...|.
T Consensus 15 Y~AQNY~VP-nv~kl~~~~~~ 34 (46)
T PF15054_consen 15 YVAQNYEVP-NVKKLAETGLD 34 (46)
T ss_pred EeeecccCC-chHHHHHHHHH
Confidence 788999996 55776666543
No 74
>PF03234 CDC37_N: Cdc37 N terminal kinase binding; InterPro: IPR013855 In Saccharomyces cerevisiae (Baker's yeast), cell division control protein Cdc37 is required for the productive formation of Cdc28-cyclin complexes. Cdc37 may be a kinase targeting subunit of Hsp90 [].
Probab=26.42 E-value=1.3e+02 Score=26.85 Aligned_cols=41 Identities=20% Similarity=0.366 Sum_probs=32.1
Q ss_pred CCCCCCCCCCHHHHHHHHHHhcCC-CCCCCHHHHHHHHHhhc
Q 024081 104 DESARSSAPKYNALIFEAISALKE-PNGSDVSAILSYIEQRL 144 (272)
Q Consensus 104 ~~~~~~shp~y~~MI~EAI~~Lke-r~GSS~~AI~kyIe~~y 144 (272)
.....+.+|+|+.||..-+..+++ +.+.+..++..+|..+.
T Consensus 99 ~~~~~~~~p~y~~Mi~~L~~qvk~~~de~~~~~~~~~l~~H~ 140 (177)
T PF03234_consen 99 VENKDPEQPTYDEMIEDLLDQVKKEPDEKSGKAELEELQEHR 140 (177)
T ss_pred cccCCCCCCCHHHHHHHHHHHHhcccCcccHHHHHHHHHHHH
Confidence 345566789999999999888875 55566888888888775
No 75
>PF00356 LacI: Bacterial regulatory proteins, lacI family; InterPro: IPR000843 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family groups together a range of proteins, including ascG, ccpA, cytR, ebgR, fruR, galR, galS, lacI, malI, opnR, purF, rafR, rbtR and scrR [, ]. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3KJX_C 1ZAY_A 1VPW_A 2PUA_A 1QQA_A 1PNR_A 1JFT_A 1QP4_A 2PUD_A 1JH9_A ....
Probab=26.23 E-value=41 Score=23.29 Aligned_cols=39 Identities=13% Similarity=0.151 Sum_probs=29.4
Q ss_pred HHhcCCCCCCCHHHHHHHHHhhcCCCccHHHHHHHHHHh
Q 024081 122 ISALKEPNGSDVSAILSYIEQRLEVPPNFRRLLSSRLRR 160 (272)
Q Consensus 122 I~~Lker~GSS~~AI~kyIe~~y~v~~nf~~~L~~~LKr 160 (272)
|..+-+.-|.|..++.++|.....+.+.-+..+...+++
T Consensus 2 i~dIA~~agvS~~TVSr~ln~~~~vs~~tr~rI~~~a~~ 40 (46)
T PF00356_consen 2 IKDIAREAGVSKSTVSRVLNGPPRVSEETRERILEAAEE 40 (46)
T ss_dssp HHHHHHHHTSSHHHHHHHHTTCSSSTHHHHHHHHHHHHH
T ss_pred HHHHHHHHCcCHHHHHHHHhCCCCCCHHHHHHHHHHHHH
Confidence 344455679999999999998877877777777666654
No 76
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=25.65 E-value=55 Score=23.92 Aligned_cols=38 Identities=8% Similarity=0.113 Sum_probs=26.2
Q ss_pred HhcCCCCCCCHHHHHHHHHhhcCCCccHHHHHHHHHHh
Q 024081 123 SALKEPNGSDVSAILSYIEQRLEVPPNFRRLLSSRLRR 160 (272)
Q Consensus 123 ~~Lker~GSS~~AI~kyIe~~y~v~~nf~~~L~~~LKr 160 (272)
..|.+.-|.|+.+|..++..+..+.+..+..+...++.
T Consensus 4 ~~iA~~~gvS~~TVSr~ln~~~~v~~~t~~~i~~~~~~ 41 (70)
T smart00354 4 KDVARLAGVSKATVSRVLNGNGRVSEETREKVLAAMEE 41 (70)
T ss_pred HHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHH
Confidence 34555668999999998887777766656666555543
No 77
>PF07106 TBPIP: Tat binding protein 1(TBP-1)-interacting protein (TBPIP); InterPro: IPR010776 This family consists of several eukaryotic TBP-1 interacting protein (TBPIP) sequences. TBP-1 has been demonstrated to interact with the human immunodeficiency virus type 1 (HIV-1) viral protein Tat, then modulate the essential replication process of HIV. In addition, TBP-1 has been shown to be a component of the 26S proteasome, a basic multiprotein complex that degrades ubiquitinated proteins in an ATP-dependent fashion. Human TBPIP interacts with human TBP-1 then modulates the inhibitory action of human TBP-1 on HIV-Tat-mediated transactivation [].
Probab=25.40 E-value=60 Score=27.76 Aligned_cols=36 Identities=25% Similarity=0.441 Sum_probs=26.7
Q ss_pred HHHHHHHHhhcC------CCccH-----HHHHHHHHHhhhccCceee
Q 024081 134 SAILSYIEQRLE------VPPNF-----RRLLSSRLRRLVAQEKLEK 169 (272)
Q Consensus 134 ~AI~kyIe~~y~------v~~nf-----~~~L~~~LKrlV~~GkLvk 169 (272)
.+|..|+...|. +-.|+ +..+..+|..||.+|+|+.
T Consensus 4 ~~Il~y~~~qNRPys~~di~~nL~~~~~K~~v~k~Ld~L~~~g~i~~ 50 (169)
T PF07106_consen 4 DAILEYMKEQNRPYSAQDIFDNLHNKVGKTAVQKALDSLVEEGKIVE 50 (169)
T ss_pred HHHHHHHHHcCCCCcHHHHHHHHHhhccHHHHHHHHHHHHhCCCeee
Confidence 578888888762 22333 3578899999999999984
No 78
>TIGR02894 DNA_bind_RsfA transcription factor, RsfA family. In a subset of endospore-forming members of the Firmcutes, members of this protein family are found, several to a genome. Two very strongly conserved sequences regions are separated by a highly variable linker region. Much of the linker region was excised from the seed alignment for this model. A characterized member is the prespore-specific transcription RsfA from Bacillus subtilis, previously called YwfN, which is controlled by sigma factor F and seems to fine-tune expression of some genes in the sigma-F regulon. A paralog in Bacillus subtilis is designated YlbO.
Probab=24.81 E-value=36 Score=29.99 Aligned_cols=50 Identities=22% Similarity=0.442 Sum_probs=36.8
Q ss_pred CCCCCHHHHHHHHHHHHhh---CCCCccccccccccCc--cCCCCCHHhHHHHHHhhccCc
Q 024081 5 KQKWTAEEEEALRAGVAKH---GTGKWKNIQRDPEFNP--FLFSRSNIDLKDKWRNMSVSA 60 (272)
Q Consensus 5 r~~WT~EEe~~L~~GV~Ky---G~GkW~~I~~~~~f~~--~l~~RT~vdLKDKWRnl~~~~ 60 (272)
...||.|||..|-+-|-+| |. +++. .|.. ---+||+.-|-=||-..+++.
T Consensus 4 QDAWT~eeDlLLAEtVLrhIReG~---TQL~---AFeEvg~~L~RTsAACGFRWNs~VRkq 58 (161)
T TIGR02894 4 QDAWTHEEDLLLAETVLRHIREGS---TQLS---AFEEVGRALNRTAAACGFRWNAYVRKQ 58 (161)
T ss_pred ccccccHHHHHHHHHHHHHHhcch---HHHH---HHHHHHHHHcccHHHhcchHHHHHHHH
Confidence 4579999999999999999 33 1221 1221 114899999999998888865
No 79
>PF02295 z-alpha: Adenosine deaminase z-alpha domain; InterPro: IPR000607 Double-stranded RNA-specific adenosine deaminase (3.5 from EC) converts multiple adenosines to inosines and creates I/U mismatched base pairs in double-helical RNA substrates without apparent sequence specificity. DRADA has been found to modify adenosines in AU-rich regions more frequently, probably due to the relative ease of melting A/U base pairs compared to G/C base pairs. The protein functions to modify viral RNA genomes, and may be responsible for hypermutation of certain negative-stranded viruses. DRADA edits the mRNAs for the glutamate receptor subunits by site-selective adenosine deamination. The DRADA repeat is also found in viral E3 proteins, which contain a double-stranded RNA-binding domain.; GO: 0003723 RNA binding, 0003726 double-stranded RNA adenosine deaminase activity; PDB: 1OYI_A 3EYI_A 2L4M_A 2HEO_D 1J75_A 1SFU_B 3IRR_B 2ACJ_C 3F22_B 2L54_A ....
Probab=24.72 E-value=1.5e+02 Score=21.99 Aligned_cols=51 Identities=27% Similarity=0.341 Sum_probs=38.3
Q ss_pred HHHHHHHHHHhcCCCCCCCHHHHHHHHHhhcCCCccHHHHHHHHHHhhhccCceeeecc
Q 024081 114 YNALIFEAISALKEPNGSDVSAILSYIEQRLEVPPNFRRLLSSRLRRLVAQEKLEKVQN 172 (272)
Q Consensus 114 y~~MI~EAI~~Lker~GSS~~AI~kyIe~~y~v~~nf~~~L~~~LKrlV~~GkLvkvK~ 172 (272)
..+.|++.|..+. |++..+|.+.+.=+ +| ++-++..|-+|-.+|.|.+..+
T Consensus 5 ~ee~Il~~L~~~g---~~~a~~ia~~~~L~--~~---kk~VN~~LY~L~k~g~v~k~~~ 55 (66)
T PF02295_consen 5 LEEKILDFLKELG---GSTATAIAKALGLS--VP---KKEVNRVLYRLEKQGKVCKEGG 55 (66)
T ss_dssp HHHHHHHHHHHHT---SSEEEHHHHHHHHT--S----HHHHHHHHHHHHHTTSEEEECS
T ss_pred HHHHHHHHHHhcC---CccHHHHHHHhCcc--hh---HHHHHHHHHHHHHCCCEeeCCC
Confidence 4678888888877 66777777666532 22 5789999999999999988654
No 80
>PF12363 DUF3647: Phage protein ; InterPro: IPR024410 Proteins in this entry are frequently annotated as phage proteins, however there is little accompanying literature to back this up or to describe the nature of these phage proteins.
Probab=24.62 E-value=2e+02 Score=23.34 Aligned_cols=53 Identities=21% Similarity=0.307 Sum_probs=37.9
Q ss_pred HHHHHHHHHHhcCCCCCCCHHHHHHHHHhhcCCCccHHHHHHHHHHhhhccCcee
Q 024081 114 YNALIFEAISALKEPNGSDVSAILSYIEQRLEVPPNFRRLLSSRLRRLVAQEKLE 168 (272)
Q Consensus 114 y~~MI~EAI~~Lker~GSS~~AI~kyIe~~y~v~~nf~~~L~~~LKrlV~~GkLv 168 (272)
+.++|.-|....+.+- |...|-.||++-+.....+..++...|+.|..+|-+.
T Consensus 53 l~d~i~~a~~~~~~~~--s~~eIe~~ie~~~e~~~~~~~l~~~vl~el~~s~~~k 105 (113)
T PF12363_consen 53 LADIIYAATAHEKKRP--SREEIEDYIEDIIEDEDDIEELFDEVLKELKKSNFFK 105 (113)
T ss_pred HHHHHHHHhcccCCCC--CHHHHHHHHHHHHhcchhHHHHHHHHHHHHHhChhHH
Confidence 4556666666665554 9999999999855444557888888888888777543
No 81
>PF13412 HTH_24: Winged helix-turn-helix DNA-binding; PDB: 1I1G_B 2IA0_B 3I4P_A 2GQQ_A 2L4A_A 2CFX_B 2DBB_B 2EFO_A 2EFQ_A 2PN6_A ....
Probab=23.52 E-value=1.5e+02 Score=19.57 Aligned_cols=37 Identities=14% Similarity=0.169 Sum_probs=24.2
Q ss_pred hcCCCCCCCHHHHHHHHHhhcCCCccHHHHHHHHHHhhhccCce
Q 024081 124 ALKEPNGSDVSAILSYIEQRLEVPPNFRRLLSSRLRRLVAQEKL 167 (272)
Q Consensus 124 ~Lker~GSS~~AI~kyIe~~y~v~~nf~~~L~~~LKrlV~~GkL 167 (272)
.|.+..|.|..-|++-+.=. ...++.+|++|+..|.|
T Consensus 11 ~l~~~~~~t~~ela~~~~is-------~~tv~~~l~~L~~~g~I 47 (48)
T PF13412_consen 11 YLRENPRITQKELAEKLGIS-------RSTVNRYLKKLEEKGLI 47 (48)
T ss_dssp HHHHCTTS-HHHHHHHHTS--------HHHHHHHHHHHHHTTSE
T ss_pred HHHHcCCCCHHHHHHHhCCC-------HHHHHHHHHHHHHCcCc
Confidence 33345557777776655411 46788999999999976
No 82
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=23.12 E-value=1.3e+02 Score=22.06 Aligned_cols=48 Identities=15% Similarity=0.187 Sum_probs=34.4
Q ss_pred HHHHHHHHHHhcCCCCCCCHHHHHHHHHhhcCCCccHHHHHHHHHHhhhccCceeeec
Q 024081 114 YNALIFEAISALKEPNGSDVSAILSYIEQRLEVPPNFRRLLSSRLRRLVAQEKLEKVQ 171 (272)
Q Consensus 114 y~~MI~EAI~~Lker~GSS~~AI~kyIe~~y~v~~nf~~~L~~~LKrlV~~GkLvkvK 171 (272)
..-.|+..|... .+.+...|..++. ++ ...++..|++|+..|-|...+
T Consensus 11 ~~~~il~~l~~~---~~~~~~~la~~~~----~s---~~~i~~~l~~L~~~g~v~~~~ 58 (101)
T smart00347 11 TQFLVLRILYEE---GPLSVSELAKRLG----VS---PSTVTRVLDRLEKKGLIRRLP 58 (101)
T ss_pred HHHHHHHHHHHc---CCcCHHHHHHHHC----CC---chhHHHHHHHHHHCCCeEecC
Confidence 455677777663 3678888877753 22 346889999999999998753
No 83
>smart00595 MADF subfamily of SANT domain.
Probab=22.81 E-value=36 Score=25.49 Aligned_cols=33 Identities=27% Similarity=0.566 Sum_probs=24.0
Q ss_pred CccccccccccCccCCCCCHHhHHHHHHhhccCchhhhcc
Q 024081 27 KWKNIQRDPEFNPFLFSRSNIDLKDKWRNMSVSAPREKSR 66 (272)
Q Consensus 27 kW~~I~~~~~f~~~l~~RT~vdLKDKWRnl~~~~~r~k~~ 66 (272)
-|..|... + +-|..+|+.||++|...-.++..+
T Consensus 29 aW~~Ia~~--l-----~~~~~~~~~kw~~LR~~y~~e~~r 61 (89)
T smart00595 29 AWEEIAEE--L-----GLSVEECKKRWKNLRDRYRRELKR 61 (89)
T ss_pred HHHHHHHH--H-----CcCHHHHHHHHHHHHHHHHHHHHH
Confidence 48888774 2 339999999999997665555444
No 84
>PF00392 GntR: Bacterial regulatory proteins, gntR family; InterPro: IPR000524 Many bacterial transcription regulation proteins bind DNA through a helix-turn-helix (HTH) motif, which can be classified into subfamilies on the basis of sequence similarities. The HTH GntR family has many members distributed among diverse bacterial groups that regulate various biological processes. It was named GntR after the Bacillus subtilis repressor of the gluconate operon []. Family members include GntR, HutC, KorA, NtaR, FadR, ExuR, FarR, DgoR and PhnF. The crystal structure of the FadR protein has been determined []. In general, these proteins contain a DNA-binding HTH domain at the N terminus, and an effector-binding or oligomerisation domain at the C terminus (IPR011711 from INTERPRO). The DNA-binding domain is well conserved in structure for the whole of the GntR family, consisting of a 3-helical bundle core with a small beta-sheet (wing); the GntR winged helix structure is similar to that found in several other transcriptional regulator families. The regions outside the DNA-binding domain are more variable and are consequently used to define GntR subfamilies []. This entry represents the N-terminal DNA-binding domain of the GntR family.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1HW1_B 1H9T_A 1HW2_A 1H9G_A 1E2X_A 3IHU_A 3C7J_A 2RA5_A 3BY6_C 3IC7_A ....
Probab=22.59 E-value=2.6e+02 Score=19.68 Aligned_cols=53 Identities=25% Similarity=0.335 Sum_probs=35.5
Q ss_pred HHHHHHHHhcCCCCCCCHHHHHHHHHhhcCCCccHHHHHHHHHHhhhccCceeeecc
Q 024081 116 ALIFEAISALKEPNGSDVSAILSYIEQRLEVPPNFRRLLSSRLRRLVAQEKLEKVQN 172 (272)
Q Consensus 116 ~MI~EAI~~Lker~GSS~~AI~kyIe~~y~v~~nf~~~L~~~LKrlV~~GkLvkvK~ 172 (272)
+.|.+.|..-.=+.|....+... |.+.|++. +.-++.+|+.|.+.|-|....|
T Consensus 7 ~~l~~~I~~g~~~~g~~lps~~~-la~~~~vs---r~tvr~al~~L~~~g~i~~~~~ 59 (64)
T PF00392_consen 7 DQLRQAILSGRLPPGDRLPSERE-LAERYGVS---RTTVREALRRLEAEGLIERRPG 59 (64)
T ss_dssp HHHHHHHHTTSS-TTSBE--HHH-HHHHHTS----HHHHHHHHHHHHHTTSEEEETT
T ss_pred HHHHHHHHcCCCCCCCEeCCHHH-HHHHhccC---CcHHHHHHHHHHHCCcEEEECC
Confidence 45677777766677776655544 44566664 5678999999999999987654
No 85
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=22.44 E-value=1.8e+02 Score=18.66 Aligned_cols=40 Identities=18% Similarity=0.214 Sum_probs=28.5
Q ss_pred CCCCCHHHHHHHHHhhcCCCccHHHHHHHHHHhhhccCceeeecccc
Q 024081 128 PNGSDVSAILSYIEQRLEVPPNFRRLLSSRLRRLVAQEKLEKVQNCF 174 (272)
Q Consensus 128 r~GSS~~AI~kyIe~~y~v~~nf~~~L~~~LKrlV~~GkLvkvK~sy 174 (272)
..+.+...|..++ +++ ...+...|+.|...|.|.+..+-+
T Consensus 12 ~~~~s~~~l~~~l----~~s---~~tv~~~l~~L~~~g~i~~~~~~~ 51 (53)
T smart00420 12 QGKVSVEELAELL----GVS---EMTIRRDLNKLEEQGLLTRVHGGA 51 (53)
T ss_pred cCCcCHHHHHHHH----CCC---HHHHHHHHHHHHHCCCEEEeecCc
Confidence 3567777777775 332 456788889999999998866543
No 86
>KOG2009 consensus Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=22.29 E-value=1.1e+02 Score=32.09 Aligned_cols=50 Identities=20% Similarity=0.359 Sum_probs=43.3
Q ss_pred CCCCCCHHHHHHHHHHHHhhCCCCccccccccccCccCCCCCHHhHHHHHHhhccCc
Q 024081 4 PKQKWTAEEEEALRAGVAKHGTGKWKNIQRDPEFNPFLFSRSNIDLKDKWRNMSVSA 60 (272)
Q Consensus 4 ~r~~WT~EEe~~L~~GV~KyG~GkW~~I~~~~~f~~~l~~RT~vdLKDKWRnl~~~~ 60 (272)
...+||.+|-+....+...+|. +.+.|... |++|...++|-|+++--+.+
T Consensus 408 ~~~~w~~se~e~fyka~~~~gs-~~slis~l------~p~R~rk~iK~K~~~eE~r~ 457 (584)
T KOG2009|consen 408 ETDKWDASETELFYKALSERGS-DFSLISNL------FPLRDRKQIKAKFKKEEKRN 457 (584)
T ss_pred ccCcccchhhHHhhhHHhhhcc-cccccccc------cccccHHHHHHHHhhhhhcc
Confidence 3568999999999999999999 99999984 58999999999998766554
No 87
>PF08944 p47_phox_C: NADPH oxidase subunit p47Phox, C terminal domain; InterPro: IPR015039 The C-terminal domain of the phagocyte NADPH oxidase subunit p47Phox contains conserved PxxP motifs that allow binding to SH3 domains, with subsequent activation of the NADPH oxidase, and generation of superoxide, which plays a crucial role in host defence against microbial infection []. ; PDB: 1K4U_P 1UEC_A.
Probab=21.10 E-value=43 Score=24.82 Aligned_cols=8 Identities=50% Similarity=1.020 Sum_probs=3.3
Q ss_pred HHHHHHhc
Q 024081 257 KEIFERCS 264 (272)
Q Consensus 257 ~ei~~~c~ 264 (272)
.+||+||+
T Consensus 38 ~~IL~RCs 45 (58)
T PF08944_consen 38 ELILQRCS 45 (58)
T ss_dssp HHHHHSS-
T ss_pred HHHHHHhh
Confidence 34455553
No 88
>PF10929 DUF2811: Protein of unknown function (DUF2811); InterPro: IPR021231 This is a bacterial family of uncharacterised proteins.
Probab=20.13 E-value=1.3e+02 Score=22.28 Aligned_cols=28 Identities=32% Similarity=0.561 Sum_probs=19.5
Q ss_pred HHHHHHHHhhcCCCccH--HHHHHHHHH-hhhccC
Q 024081 134 SAILSYIEQRLEVPPNF--RRLLSSRLR-RLVAQE 165 (272)
Q Consensus 134 ~AI~kyIe~~y~v~~nf--~~~L~~~LK-rlV~~G 165 (272)
++++.||+.+ |++ .+++..+|. -|+.+|
T Consensus 12 ~~m~~fie~h----P~WDQ~Rl~~aALa~FL~QnG 42 (57)
T PF10929_consen 12 QAMKDFIETH----PNWDQYRLFQAALAGFLLQNG 42 (57)
T ss_pred HHHHHHHHcC----CCchHHHHHHHHHHHHHHHcC
Confidence 5788999988 444 477888883 455555
No 89
>PF12029 DUF3516: Domain of unknown function (DUF3516); InterPro: IPR021904 This presumed domain is functionally uncharacterised. This domain is found in bacteria. This domain is typically between 460 to 473 amino acids in length. This domain is found associated with PF00270 from PFAM, PF00271 from PFAM.
Probab=20.12 E-value=2.1e+02 Score=29.29 Aligned_cols=53 Identities=19% Similarity=0.379 Sum_probs=44.4
Q ss_pred HHHHHHHHHhcCCCCCCCHHHHHHHHHhhcCCCccHHHHHHHHH---HhhhccCceeeec
Q 024081 115 NALIFEAISALKEPNGSDVSAILSYIEQRLEVPPNFRRLLSSRL---RRLVAQEKLEKVQ 171 (272)
Q Consensus 115 ~~MI~EAI~~Lker~GSS~~AI~kyIe~~y~v~~nf~~~L~~~L---KrlV~~GkLvkvK 171 (272)
..||+.-| .|.|-...++...|.+||+.+..-++++..++ +.|+..|.++++.
T Consensus 61 haMlLnvl----~r~gd~~~~~~~Ll~~nhe~~~~~~~~~~ra~~i~r~L~~agvve~~~ 116 (461)
T PF12029_consen 61 HAMLLNVL----ARPGDAFAAMRHLLRDNHEPRARQRRLIRRAIEIYRSLLDAGVVERLP 116 (461)
T ss_pred HHHHHHHH----cCCCcHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHhCCCEEEec
Confidence 46776666 78999999999999999988777777777776 8999999999853
No 90
>PF08671 SinI: Anti-repressor SinI; InterPro: IPR010981 The SinR repressor is part of a group of Sin (sporulation inhibition) proteins in Bacillus subtilis that regulate the commitment to sporulation in response to extreme adversity []. SinR is a tetrameric repressor protein that binds to the promoters of genes essential for entry into sporulation and prevents their transcription. This repression is overcome through the activity of SinI, which disrupts the SinR tetramer through the formation of a SinI-SinR heterodimer, thereby allowing sporulation to proceed. The SinR structure consists of two domains: a dimerisation domain stabilised by a hydrophobic core, and a DNA-binding domain that is identical to domains of the bacteriophage 434 CI and Cro proteins that regulate prophage induction. The dimerisation domain is a four-helical bundle formed from two helices from the C-terminal residues of SinR and two helices from the central residues of SinI. These regions in SinR and SinI are similar in both structure and sequence. The interaction of SinR monomers to form tetramers is weaker than between SinR and SinI, since SinI can effectively disrupt SinR tetramers. This entry represents the dimerisation domain in both SinI and SinR proteins.; GO: 0005488 binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1B0N_A 2YAL_A.
Probab=20.09 E-value=2e+02 Score=18.49 Aligned_cols=25 Identities=28% Similarity=0.355 Sum_probs=18.6
Q ss_pred HHHHHHHHHHhcCCCCCCCHHHHHHHHHhh
Q 024081 114 YNALIFEAISALKEPNGSDVSAILSYIEQR 143 (272)
Q Consensus 114 y~~MI~EAI~~Lker~GSS~~AI~kyIe~~ 143 (272)
+-.+|.||+.. |.|..-|..|++.+
T Consensus 5 W~~Li~eA~~~-----Gls~eeir~FL~~~ 29 (30)
T PF08671_consen 5 WVELIKEAKES-----GLSKEEIREFLEFN 29 (30)
T ss_dssp HHHHHHHHHHT-----T--HHHHHHHHHHH
T ss_pred HHHHHHHHHHc-----CCCHHHHHHHHHhC
Confidence 45788898874 99999999999754
Done!